********>Master Bugfix File - AmberTools bugfixes for version 1.4, fixes 1-16

Programs: AmberTools

Description: This is the master bugfix file for AmberTools-1.4. It
             contains all of the bugfixes released against version 1.4
             in a single patch script.

Usage: Save this file in your $AMBERHOME directory and then 
       apply this patch file to your distribution as follows:

cd $AMBERHOME
patch -p0 -N <bugfix.all

If you have already patched some files the patch program should realise this
and skip them. If you have trouble then you may need to apply each of the
bug fixes separately.

-----------------------------------------------------------------------------

********> bugfix 1
Author: Junmei Wang
Date:   30 April 2010

Programs: gaff.dat

Description:  This patch adds the "cz" atom type to the list of atoms, and
    cleans ups to someunsed parameters.

Fix:  Apply the following fix to amber11/dat/leap/parm/gaff.dat

---------------------------------------------------------------------------
--- dat/leap/parm/gaff.dat	2010-04-29 16:14:08.000000000 -0400
+++ dat/leap/parm/gaff.dat	2010-04-30 07:38:51.000000000 -0400
@@ -16,6 +16,7 @@
 cy 12.01         0.360               Sp3 carbons in square systems
 cu 12.01         0.360               Sp2 carbons in triangle systems
 cv 12.01         0.360               Sp2 carbons in square systems
+cz 12.01         0.360               Sp2 carbon in guanidine group
 h1 1.008         0.135               H bonded to aliphatic carbon with 1 electrwd. group  
 h2 1.008         0.135               H bonded to aliphatic carbon with 2 electrwd. group 
 h3 1.008         0.135               H bonded to aliphatic carbon with 3 electrwd. group 
@@ -852,11 +853,6 @@
 s6-ss  139.6    2.1180       SOURCE3       5	0.0209
 sh-sh  158.9    2.0580       SOURCE2       1	0.0000
 sh-ss  155.8    2.0670       SOURCE3       3	0.0029
-Si-c3  189.8    1.8928       SOURCE4      77	0.0061
-Si-ca  191.1    1.8898       SOURCE4      11	0.0028
-Si-ha  186.3    1.4887       SOURCE4       6	0.0040
-Si-oh  267.6    1.6792       SOURCE4       6	0.0035
-Si-os  287.7    1.6524       SOURCE4      22	0.0057
 s -s   169.0    2.0300       SOURCE3       1	0.0000
 s -s2  229.2    1.8970       SOURCE1       5	0.0000
 s -s4  152.8    2.0760       SOURCE3       4	0.0345
@@ -1091,7 +1087,6 @@
 hc-c2-s6   54.150     115.450	SOURCE3            1	
 hc-c2-sh   53.550     115.630	SOURCE3            1	
 hc-c2-ss   54.900     115.620	SOURCE3            1	
-hn-c2-n4    0.000     112.740	SOURCE3            1	
 hx-c2-n4   48.420     113.030	SOURCE3            3	0.3873
 i -c2-i    60.960     117.940	SOURCE3            1	0.0000
 n1-c2-n1   73.610     124.150	HF/6-31G*          1	
@@ -1464,9 +1459,6 @@
 s6-c3-s6  102.050     111.750	SOURCE3            1	0.0000
 sh-c3-sh   97.420     116.260	SOURCE3            1	0.0000
 sh-c3-ss   99.850     110.730	SOURCE3            1	
-Si-c3-c3   74.610     114.340	SOURCE4           26	1.1613
-Si-c3-h1   51.040     110.900	SOURCE4           17	1.0270
-Si-c3-hc   50.960     111.210	SOURCE4          222	0.4865
 s -c3-s    93.400     123.350	SOURCE3            1	0.0000
 ss-c3-ss   99.950     110.570	SOURCE4           15	1.4311
 br-ca-br   67.310     117.600	SOURCE3            1	
@@ -1500,7 +1492,6 @@
 ca-ca-i    58.590     118.470	SOURCE3           10	0.6181
 ca-ca-n1   68.920     118.500	HF/6-31G*          1	
 ca-ca-n2   70.950     119.570	SOURCE3            1	
-ca-ca-n3    0.000     121.190	SOURCE3            1	
 ca-ca-n4   67.280     118.410	SOURCE3            6	0.1691
 ca-ca-n    67.970     119.890	SOURCE3           18	0.2095
 ca-ca-na   70.210     118.340	SOURCE3           54	3.6168
@@ -1540,7 +1531,6 @@
 cf-ca-nb   68.080     118.140	SOURCE4           12	1.1775
 cg-ca-cp   65.330     121.530	SOURCE4           12	0.1831
 c -ca-ha   46.510     115.900	SOURCE3            1	
-c -ca-hc    0.000     120.000	SOURCE3            1	
 cl-ca-cl   62.630     118.720	SOURCE3            1	
 cl-ca-cp   62.600     120.310	SOURCE4           18	0.5607
 cl-ca-nb   65.810     116.150	SOURCE4           50	0.6047
@@ -1606,7 +1596,6 @@
 s4-ca-s4  104.060     105.810	SOURCE3            1	
 s6-ca-s6  105.770     105.810	SOURCE3            1	
 sh-ca-sh   98.150     120.240	SOURCE3            1	
-Si-ca-ca   73.850     121.430	SOURCE4           19	0.4235
 s -ca-s    98.380     125.140	SOURCE3            1	
 ss-ca-ss  100.760     115.150	SOURCE3            1	
 br-c -br   66.910     113.100	SOURCE3            1	
@@ -1636,7 +1625,6 @@
 c3-c -n    67.860     115.150	SOURCE3          153	2.7443
 c3-c -ne   68.090     111.390	SOURCE4           11	2.1430
 c3-c -nf   67.430     113.380	SOURCE3            1	same_as_c3-c-ne
-c3-c -nh    0.000     113.580	SOURCE3            1	
 c3-c -o    68.030     123.110	SOURCE3          267	3.0977
 c3-c -oh   69.840     112.200	SOURCE3           14	1.8324
 c3-c -os   69.260     111.960	SOURCE3           15	2.3072
@@ -1832,7 +1820,6 @@
 ha-cc-os   52.490     110.860	SOURCE3            7	1.3846
 ha-cc-pd   42.350     121.760	SOURCE3           84	same_as_ha-cd-pc
 ha-cc-ss   53.490     121.640	SOURCE2            5	1.3276
-c -c -hc    0.000     117.080	SOURCE3            1	
 ch-c -ch   65.440     115.380	SOURCE3            1	same_as_cg-c-cg
 ch-c -ha   47.800     113.900	SOURCE2            1	same_as_cg-c-ha
 ch-c -o    70.210     122.310	SOURCE3            2	same_as_cg-c-o
@@ -2183,7 +2170,6 @@
 c -cf-n    66.600     116.790	SOURCE4            8	0.8255
 c -cf-nh   65.940     122.760	SOURCE3            1	same_as_c-ce-nh
 f -c -f    72.220     107.350	SOURCE2            2	0.2500
-f -c -h     0.000     109.900	SOURCE2            1	0.0000
 h4-cf-n2   52.210     122.140	SOURCE4           11	0.9297
 h4-cf-ne   52.280     120.210	SOURCE4            6	0.8104
 ha-cf-n1   52.480     115.960	SOURCE3            2	3.5425
@@ -2239,34 +2225,20 @@
 cf-ch-cg   57.400     177.900	SOURCE4            8	0.4883
 cf-ch-n1   59.370     178.120	SOURCE4           22	1.5200
 cg-ch-ch   58.680     179.670	SOURCE4            7	0.1439
-hc-c -hc    0.000     115.680	SOURCE3            1	
-hc-c -n     0.000     120.000	SOURCE3            1	
-hc-c -nh    0.000     112.700	SOURCE3            1	
-hc-c -o     0.000     120.000	SOURCE3            1	
-hc-c -oh    0.000     113.700	SOURCE3            1	
-hc-c -os    0.000     113.580	SOURCE3            1	
 n1-ch-nf   64.660     176.170	SOURCE2            3	same_as_n1-cg-ne
-h -c -o     0.000     127.300	SOURCE2            1	0.0000
 i -c -i    59.790     116.450	SOURCE3            1	0.0000
 i -c -o    55.510     122.020	SOURCE3            4	1.2961
 f -cl-f    50.000      87.500	SOURCE2            1	estimated_force_constant
 n2-c -n2   71.830     110.310	SOURCE3            1	
-n2-c -na    0.000     118.600	SOURCE3            1	
 n2-c -o    73.020     122.500	SOURCE3            1	
-n3-c -n3    0.000     112.980	SOURCE3            1	
-n3-c -o     0.000     122.260	SOURCE3            1	
 n4-c -n4   64.710     114.640	SOURCE3            1	0.0000
 n4-c -o    69.580     118.830	SOURCE3            4	3.8516
-na-c -na    0.000     115.400	SOURCE3            1	
-na-c -o     0.000     122.850	SOURCE3            1	
 nc-c -o    74.050     123.980	SOURCE4           66	0.9502
 nd-c -o    73.720     121.760	SOURCE4           55	1.1138
 ne-c -ne   73.220     110.310	SOURCE3            1	0.0000
 ne-c -o    72.940     126.030	SOURCE4           39	0.9885
 nf-c -nf   73.070     110.310	SOURCE3            1	same_as_ne-c-ne
 nf-c -o    73.320     124.390	SOURCE3            3	same_as_ne-c-o
-nh-c -nh    0.000     110.980	SOURCE3            1	
-nh-c -o     0.000     124.620	SOURCE3            1	
 n -c -n    74.800     113.380	SOURCE4          635	1.4358
 n -c -nc   72.690     117.050	SOURCE4           54	0.7020
 n -c -nd   71.900     117.060	SOURCE4           23	0.9856
@@ -2318,10 +2290,10 @@
 py-c -py   57.520     123.800	SOURCE3            1	0.0000
 ca-cq-ca   67.000     118.240	SOURCE4            5	0.2181
 ca-cq-cq   64.220     120.410	SOURCE4           12	1.4029
-ca-cq-nb    0.000     122.970	SOURCE3            2	0.0000
+ca-cq-nb   69.270     121.650	SOURCE4           63	same as ca-cp-nb
 cp-cq-cq   62.640     124.470	SOURCE4            5	1.0864
 cq-cq-cq   72.200      90.000	SOURCE3            4	0.0000
-cq-cq-nb    0.000     116.430	SOURCE3            2	0.0000
+cq-cq-nb   68.050     116.600	SOURCE4           88	same as cp-cp-nb
 s4-c -s4   98.110     108.810	SOURCE3            1	
 s6-c -s6   95.130     115.750	SOURCE3            1	
 sh-c -sh  100.060     115.330	SOURCE3            1	0.0000
@@ -2454,9 +2426,6 @@
 n -cy-s6   82.570     103.450	SOURCE4            6	0.7197
 n -cy-ss   82.030     105.120	SOURCE4           69	0.3987
 nh-cz-nh   72.970     120.170	SOURCE4           26	0.3964
-ca-i -cl    0.000      90.210	SOURCE3            2	estimated_force_constant
-ca-i -o     0.000      97.080	SOURCE3            5	0.2233,estimated_force_constant
-cl-i -cl    0.000     179.580	SOURCE3            1	estimated_force_constant
 br-n1-c1   51.100     180.000	HF/6-31G*          1	
 c1-n1-c1   64.910     179.920	HF/6-31G*          1	
 c1-n1-c2   60.250     177.730	HF/6-31G*          1	
@@ -2729,7 +2698,6 @@
 c2-n3-c2   66.220     124.680	SOURCE3            1	
 c2-n3-hn   49.110     119.380	SOURCE3            1	
 c3-n3-c3   64.010     110.900	SOURCE3           40	2.3048
-c3-n3-ca    0.000     116.390	SOURCE3            1	
 c3-n3-cl   62.170     107.230	SOURCE3            3	0.3673
 c3-n3-cx   62.450     116.320	SOURCE4           24	0.5119
 c3-n3-cy   61.690     118.260	SOURCE4           14	0.8788
@@ -2753,7 +2721,6 @@
 c3-n3-sh   78.550     112.700	SOURCE3            1	0.0000
 c3-n3-ss   77.950     116.010	SOURCE3            3	1.1944
 c3-n3-sy   79.010     115.270	SOURCE4          108	1.7647
-c -n3-c     0.000     127.170	SOURCE3            1	
 cl-n3-cl   61.850     108.280	SOURCE3            1	0.0000
 cl-n3-hn   42.590     104.390	SOURCE3            2	0.0000
 cl-n3-n3   63.750     107.650	SOURCE3            1	0.0000
@@ -2824,7 +2791,6 @@
 c1-n4-hn   48.620     110.190	SOURCE3            7	1.0847
 c2-n4-c2   63.010     112.580	SOURCE3            1	0.0000
 c2-n4-c3   63.100     110.960	SOURCE4           13	2.4632
-c2-n4-h4    0.000     112.460	SOURCE3            1	
 c2-n4-hn   46.430     111.360	SOURCE3           13	1.2672
 c3-n4-c3   62.840     110.640	SOURCE3           13	1.3060
 c3-n4-ca   63.610     110.400	SOURCE4           46	1.4643
@@ -3002,10 +2968,6 @@
 ca-na-s    75.010     125.640	SOURCE3            1	
 ca-na-sh   76.630     125.440	SOURCE3            1	
 ca-na-ss   74.880     129.910	SOURCE4            8	0.1449
-c -na-c     0.000     126.400	SOURCE3            1	
-c -na-c2    0.000     125.090	SOURCE3            1	
-c -na-c3    0.000     117.600	SOURCE3            1	
-c -na-ca    0.000     125.200	SOURCE3            1	
 cc-na-cc   68.940     109.900	SOURCE3          109	1.5547
 cc-na-cd   63.880     128.010	SOURCE3            1	0.0000
 cc-na-ce   63.050     126.610	SOURCE4            8	0.5158
@@ -3058,7 +3020,6 @@
 cd-na-s    74.800     125.660	SOURCE3            8	0.1880
 cd-na-sh   76.830     123.960	SOURCE3           10	0.3424
 cd-na-ss   77.930     119.180	SOURCE3           36	5.0538
-c -na-hn    0.000     118.000	SOURCE3            1	
 cl-na-cl   56.330     122.800	SOURCE3            1	
 cl-na-nc   59.890     119.360	SOURCE3            4	1.7128
 cl-na-nd   59.890     119.360	SOURCE3            4	same_as_cl-na-nc
@@ -3067,7 +3028,6 @@
 cl-na-pc   58.780     120.510	SOURCE3            3	2.1985
 cl-na-pd   58.780     120.510	SOURCE3            3	same_as_cl-na-pc
 cl-na-ss   77.180     111.910	SOURCE3            1	0.0000
-c -na-n     0.000     124.660	SOURCE3            1	
 f -na-f    62.220     120.200	SOURCE3            1	
 f -na-nc   66.640     118.050	SOURCE3            4	1.7931
 f -na-nd   66.640     118.050	SOURCE3            4	same_as_f-na-nc
@@ -3231,7 +3191,7 @@
 sy-na-sy   96.930     123.200	SOURCE3            1	
 ca-nb-ca   68.590     115.860	SOURCE3           46	1.1645
 ca-nb-cp   68.010     118.040	SOURCE4           58	0.7819
-ca-nb-cq    0.000     117.040	SOURCE3            2	0.0000
+ca-nb-cq   68.010     118.040	SOURCE4           58	same as ca-nb-cp
 ca-nb-nb   69.370     118.890	SOURCE3           10	0.6031
 cp-nb-nb   68.790     121.110	SOURCE4           12	0.4315
 nb-nb-nb   70.440     121.040	SOURCE3            1	0.0000
@@ -3597,8 +3557,6 @@
 ca-nh-sh   78.190     121.410	SOURCE3            1	0.0000
 ca-nh-ss   78.160     121.500	SOURCE3            3	2.6255
 ca-nh-sy   76.750     125.260	SOURCE4           41	1.7517
-c -nh-c     0.000     119.570	SOURCE3            1	
-c -nh-ca    0.000     123.570	SOURCE3            1	
 cc-nh-cx   63.320     122.820	SOURCE4           42	1.1841
 cc-nh-hn   48.860     117.160	SOURCE3           11	2.6137
 cc-nh-n2   68.230     119.660	SOURCE4            5	1.3903
@@ -3610,10 +3568,8 @@
 ce-nh-sy   80.450     112.970	SOURCE4            7	1.0636
 cf-nh-hn   48.620     115.620	SOURCE4           16	1.3549
 cf-nh-o    67.070     129.430	SOURCE3            1	same_as_ce-nh-o
-c -nh-hn    0.000     115.730	SOURCE3            1	
 cl-nh-cl   62.930     106.600	SOURCE3            1	
 cl-nh-hn   43.080     104.140	SOURCE3            1	0.0000
-c -nh-n4    0.000     111.350	SOURCE3            1	
 cx-nh-cx   86.530      62.020	SOURCE4           45	0.6189
 cx-nh-hn   45.790     118.890	SOURCE4            8	0.1391
 cz-nh-hn   48.790     121.240	SOURCE4           40	0.5682
@@ -3783,7 +3739,6 @@
 ho-oh-sh   54.390     106.240	SOURCE3            2	0.0661
 ho-oh-ss   54.540     107.060	SOURCE3            4	0.9967
 ho-oh-sy   55.940     106.410	SOURCE4           33	0.3729
-Si-oh-ho   52.570     115.710	SOURCE4            5	0.1738
 br-os-br   65.080     110.630	SOURCE3            1	0.0000
 c1-os-c1   66.990     115.020	SOURCE3            1	0.0000
 c1-os-c3   64.470     113.390	SOURCE3            1	0.0000
@@ -3892,7 +3847,6 @@
 s4-os-s4   99.450     111.630	SOURCE3            1	0.0000
 s6-os-s6  103.740     119.070	SOURCE3            2	0.4318
 sh-os-sh   97.950     118.950	SOURCE3            1	0.0000
-Si-os-c3   74.830     124.640	SOURCE4            9	0.2879
 s -os-s    91.270     118.080	SOURCE3            1	0.0000
 ss-os-ss   97.420     115.640	SOURCE3            1	0.0000
 br-p2-br   65.020     108.600	SOURCE3            1	
@@ -4615,7 +4569,6 @@
 f -s4-f    43.790      92.710	SOURCE2            3	0.1490
 f -s4-o    43.870     106.810	SOURCE2            2	0.0100
 f -s4-s    47.340     107.500	SOURCE2            1	0.0000
-hn-s4-hs    0.000      86.990	SOURCE3            1	
 hs-s4-hs   23.650      87.000	SOURCE3            2	0.0202
 hs-s4-n1   32.050      90.510	HF/6-31G*          1	
 hs-s4-o    31.160     110.270	SOURCE3            5	0.1908
@@ -4789,12 +4742,6 @@
 hs-sh-s6   33.980      93.830	SOURCE3            3	1.2561
 hs-sh-sh   33.890      99.070	SOURCE3            2	0.0000
 hs-sh-ss   33.730      99.170	SOURCE3            3	0.2457
-c3-Si-c3   34.810     109.820	SOURCE4           88	0.5569
-c3-Si-ca   34.800     110.090	SOURCE4           26	0.7331
-c3-Si-oh   38.160     107.440	SOURCE4            8	1.5150
-c3-Si-os   38.140     108.750	SOURCE4           38	0.7301
-ha-Si-ha   19.530     108.770	SOURCE4            5	0.5372
-os-Si-os   42.630     108.350	SOURCE4           15	1.7995
 br-ss-br   41.920     102.920	SOURCE3            1	0.0000
 br-ss-c3   39.460      99.030	SOURCE3            1	0.0000
 c1-ss-c1   41.480      98.300	SOURCE2            1	0.0000
@@ -4813,7 +4760,6 @@
 c3-ss-cl   37.940      99.400	SOURCE2            1	0.0000
 c3-ss-cy   38.750      94.320	SOURCE4           62	0.3646
 c3-ss-f    39.670      97.490	SOURCE3            1	0.0000
-c3-ss-ha    0.000      96.500	SOURCE2            1	0.0000
 c3-ss-i    35.060     100.000	SOURCE3            1	0.0000
 c3-ss-n1   41.250      98.440	HF/6-31G*          1	
 c3-ss-n2   41.260      96.420	SOURCE3            5	1.3604
@@ -5883,7 +5829,7 @@
 were replaced with those newly generated. Here are the numbers:
 
 Bond length: 59 low quality parameters were replaced and 56 new parameters
-were introduced. $j
+were introduced.
 
 Bond angle:  437 low quality parameters were replaced and 618 new
 parameters were introduced.
---------------------------------------------------------------------------
Workarounds:  none

********> bugfix 2
Author: Wei Zhang
Date:   28 May 2010

Programs: sleap

Description:  Under some circumstances, the addions command can cause a
    segfault.

Fix:  Apply the following fix to
      amber11/AmberTools/src/gleap/mortsrc/capbox/addions.cpp

---------------------------------------------------------------------------
--- AmberTools/src/gleap/mortsrc/capbox/addions.cpp
+++ AmberTools/src/gleap/mortsrc/capbox/addions.cpp
@@ -85,6 +85,7 @@ namespace mort
     {
         mort_ionee ionee(m);
         addions_core( ionee, ion, num_ion, shlext, resolution );
+	m.cleanup();
     }
 
     void addions_core( ionee_i& ionee, const molecule_t& ion, int num_ion, double shlext, double resolution )
---------------------------------------------------------------------------
Workarounds:  none

********> bugfix 3
Author: Mengjuei Hsieh
Date:   1 June 2010

Programs: tleap, xleap

Description:  LEaP has some strcpy() calls with overlapping memory, which
      leads to problems with Fedora Core x86_64, and maybe with Ubuntu 10.04.

Fix:  Apply the following fix in amber11/AmberTools/src/leap/src/leap

---------------------------------------------------------------------------
--- AmberTools/src/leap/src/leap/basics.c
+++ AmberTools/src/leap/src/leap/basics.c
@@ -462,7 +462,7 @@ char		*cPBlock;
     SmPMallocList = mPMem;
     
     sTrailer = ((char*)mPMem)+sizeof(MEMHEADER)+lSize;
-    memcpy( sTrailer, mPMem->sCheck, TRAILERLEN );
+    memmove( sTrailer, mPMem->sCheck, TRAILERLEN );
     
     return ((char*)mPMem) + sizeof(MEMHEADER);
 }
@@ -528,7 +528,7 @@ char		*sTrailer;
     if ( mPMem == NULL ) {
         DFATAL(( "Could not malloc in REALLOC: %s\n", strerror(errno) ));
     }
-    memcpy( mPMem, mPPrevious, 
+    memmove( mPMem, mPPrevious, 
            MIN( lSize, mPPrevious->lSize) + sizeof(MEMHEADER)+TRAILERLEN );
                      
     strcpy( mPPrevious->sCheck, FREESTR );
@@ -540,7 +540,8 @@ char		*sTrailer;
                 /* Fill the trailer */
     
     sTrailer = ((char*)mPMem)+sizeof(MEMHEADER)+lSize;
-    strcpy( sTrailer, mPMem->sCheck );
+    memmove( sTrailer, mPMem->sCheck, strlen(mPMem->sCheck) );
+    sTrailer[strlen(mPMem->sCheck)]='\0';
     
     return ((char*)mPMem) + sizeof(MEMHEADER);
 }
--- AmberTools/src/leap/src/leap/database.c
+++ AmberTools/src/leap/src/leap/database.c
@@ -594,6 +594,7 @@ static char *
 sStripString( char *sLine, char *sStr )
 {
 char            c, *sCur, *sStart;
+int             mylength;
 
     sCur = sLine;
     sStart = sStr;
@@ -615,8 +616,10 @@ char            c, *sCur, *sStart;
         (*sStr++) = c;
     } while ( (*sCur) != '\0' );
     *sStr = '\0';
-    strcpy( sLine, sCur );
-    
+    mylength=strlen(sCur);
+    //strcpy( sLine, sCur );
+    memmove(sLine, sCur, mylength);
+    sLine[mylength]='\0';
     return(sStart);
 }
 
--- AmberTools/src/leap/src/leap/sort.c
+++ AmberTools/src/leap/src/leap/sort.c
@@ -217,9 +217,9 @@ int		iTopTrue, iBottomFalse;
 		/* If false then swap it with the bottom of the false */
 		/* group, and leave the current pointer where it is  */
 
-	    memcpy( PSwapBuffer, PCur, iElementSize );
-	    memcpy( PCur, PTop, iElementSize );
-	    memcpy( PTop, PSwapBuffer, iElementSize );
+	    memmove( PSwapBuffer, PCur, iElementSize );
+	    memmove( PCur, PTop, iElementSize );
+	    memmove( PTop, PSwapBuffer, iElementSize );
 
 	    PTop = (char*)PTop - iElementSize;
 	    iBottomFalse--;
--- AmberTools/src/leap/src/leap/stringExtra.c
+++ AmberTools/src/leap/src/leap/stringExtra.c
@@ -130,10 +130,13 @@ char *
 sRemoveLeadingSpaces( char *sLine )
 {
 char	*sTemp;
-
+int      mylength;
     sTemp = sLine;
     while ( (*sTemp==' ') && ( *sTemp!='\0' )) sTemp++;
-    strcpy( sLine, sTemp );
+    mylength=strlen(sTemp);
+    //strcpy( sLine, sTemp );
+    memmove(sLine, sTemp, mylength);
+    sLine[mylength]='\0';
     return(sLine);
 }
 
@@ -152,6 +155,7 @@ void
 sRemoveFirstString( char *sLine, char *sHead )
 {
 char	*sTemp;
+int      mylength;
 
     sTemp = sLine;
     while ( (*sTemp!=' ') && ( *sTemp!='\0' )) sTemp++;
@@ -163,7 +167,11 @@ char	*sTemp;
     *sTemp = '\0';
     strcpy( sHead, sLine );
     sTemp++;
-    strcpy( sLine, sTemp );
+    mylength=strlen(sTemp);
+    //strcpy( sLine, sTemp );
+    memmove(sLine, sTemp, mylength);
+    sLine[mylength]='\0';
+    
 }
 
 
--- AmberTools/src/leap/src/leap/xaCommand.c
+++ AmberTools/src/leap/src/leap/xaCommand.c
@@ -837,7 +837,7 @@ STRING		sName;
      *	at the top of the list
      */
     qsort( saPNames, iNumber, sizeof(STRING), 
-		(int (*) (void *, void *) )ziXACCompareTwoDirectoryEntries );
+		(int (*) (const void *, const void *) )ziXACCompareTwoDirectoryEntries );
 
     /*
      *  Reformulate as an array of pointers to char
---------------------------------------------------------------------------
Workarounds:  none

********> bugfix 4
Author: Daniel R. Roe
Date: 2010-05-27

Description:
Fixes bug where ptraj actions would attempt to allocate a negative number of 
bytes of memory when the number of frames to be read is unknown, i.e. file is 
compressed or corrupted. The number of frames for compressed files can now be
calculated ahead of time. For gzip files this is simple, but for bzip2 and 
zip files this adds to the processing time since uncompressed file size cannot
be determined for these file types without external programs. For corrupted 
files the trajectory filesize is used to predict the number of frames.
After applying the patch ptraj should be completely recompiled (i.e. perform
a make clean in the ptraj directory).

To apply the patch:
cd $AMBERHOME
patch -p0 -N < bugfix.4

-----------------------------------------------------------------------------
--- AmberTools/src/ptraj/trajectory.h	2010-03-30 23:05:16.000000000 -0400
+++ AmberTools/src/ptraj/trajectory.h	2010-05-27 11:16:27.928920475 -0400
@@ -168,6 +168,7 @@
   char *filename;  // File name
   int start;       // Frame to start processing
   int stop;        // Frame to end processing
+  int Nframes;     // Total number of frames in the file.
   int offset;      // # of frames to skip
   int append;      // File will be appended to
   int isBox;       // File has box information
@@ -230,6 +231,7 @@
   _p_->filename = NULL; \
   _p_->start = 1; \
   _p_->stop = -1; \
+  _p_->Nframes = 0; \
   _p_->offset = 1; \
   _p_->append = 0; \
   _p_->isBox = 0; \
--- AmberTools/src/ptraj/io.c	2010-03-30 23:05:16.000000000 -0400
+++ AmberTools/src/ptraj/io.c	2010-05-27 15:15:49.825241972 -0400
@@ -674,6 +674,91 @@
 }
 
 /* DAN ROE:
+ * gzipFileSize()
+ * Return the uncompressed size in bytes of gzipped file by peeking at the 
+ * last 4 bytes.
+ */
+int gzipFileSize(char *filename) {
+  FILE *infile;
+  int b1,b2,b3,b4,val;
+
+  if (filename==NULL) return -1;
+  if ( (infile = fopen(filename,"rb"))==NULL ) {
+    fprintf(stdout,"Error: gzipFileSize: Could not open %s for reading.\n",filename);
+    return -1;
+  }
+
+  // Place 4 bytes from the end
+  fseek(infile, -4, SEEK_END);
+
+  b1=0; b2=0; b3=0; b4=0;
+  fread(&b4,1,1,infile);
+  fread(&b3,1,1,infile);
+  fread(&b2,1,1,infile);
+  fread(&b1,1,1,infile);
+
+  val = (b1 << 24) | (b2 << 16) + (b3 << 8) + b4;
+
+  fclose(infile);
+
+  if (prnlev>0) fprintf(stdout,"gzipFileSize: Uncompressed size of %s: %i\n",filename,val);
+
+  return val;
+}
+/* DAN ROE: 
+ * bzip2FileSize()
+ * Return the uncompressed size of bzip2 file in bytes by counting all 
+ * characters using bzcat and wc.
+ */
+int bzip2FileSize(char *filename) {
+  int val;
+  char *command;
+  FILE *pipe;
+
+  if (filename==NULL) return -1;
+  // Use bzcat <file> | wc -c to calc file size
+  command=(char*) malloc( (15 + strlen(filename)) * sizeof(char));
+  sprintf(command,"bzcat %s | wc -c",filename);
+  if ((pipe=popen(command,"r"))==NULL) {
+    fprintf(stdout,"Error: bzip2FileSize: Could not open %s for reading.\n",filename);
+    fprintf(stdout,"       Check that bzcat and wc are present on your system.\n");
+    return -1;
+  }
+  fscanf(pipe,"%i",&val);
+  pclose(pipe);
+
+  if (prnlev>0) fprintf(stdout,"bzip2FileSize: Uncompressed size of %s: %i\n",filename,val);
+
+  return val;
+}
+/* DAN ROE: 
+ * zipFileSize()
+ * Return the uncompressed size of zip file in bytes by counting all 
+ * characters using unzip and wc.
+ */
+int zipFileSize(char *filename) {
+  int val;
+  char *command;
+  FILE *pipe;
+
+  if (filename==NULL) return -1;
+  // Use unzip -p <file> | wc -c to calc file size
+  command=(char*) malloc( (18 + strlen(filename)) * sizeof(char));
+  sprintf(command,"unzip -p %s | wc -c",filename);
+  if ((pipe=popen(command,"r"))==NULL) {
+    fprintf(stdout,"Error: zipFileSize: Could not open %s for reading.\n",filename);
+    fprintf(stdout,"       Check that unzip and wc are present on your system.\n");
+    return -1;
+  }
+  fscanf(pipe,"%i",&val);
+  pclose(pipe);
+
+  if (prnlev>0) fprintf(stdout,"zipFileSize: Uncompressed size of %s: %i\n",filename,val);
+
+  return val;
+}
+
+/* DAN ROE:
  * id_Filesig(): Attempt to identify the file type by first 3 hex vals.
  * A filename or an open stream should be supplied.
  * If a filename is supplied, the file is opened, checked, then closed.
--- AmberTools/src/ptraj/io.h	2010-03-30 23:05:16.000000000 -0400
+++ AmberTools/src/ptraj/io.h	2010-05-27 15:16:16.839329069 -0400
@@ -76,6 +76,9 @@
 
 extern void doSystem(char *);
 extern char * promptToOpenFile( FILE **, char *, char *, char *);
+extern int gzipFileSize(char *);
+extern int bzip2FileSize(char *);
+extern int zipFileSize(char *);
 extern int id_Filesig(char *,FILE *);
 extern int openFile( FILE **, char *, char *);
 extern int  promptUserResponse(FILE *, FILE *, char *, char *, int);
@@ -94,6 +97,9 @@
 
 extern void doSystem();
 extern char * promptToOpenFile();
+extern int gzipFileSize();
+extern int bzip2FileSize();
+extern int zipFileSize();
 extern int id_Filesig();
 extern int openFile();
 extern int  promptUserResponse();
--- AmberTools/src/ptraj/ptraj.c	2010-04-23 10:17:17.000000000 -0400
+++ AmberTools/src/ptraj/ptraj.c	2010-05-27 15:16:27.913954807 -0400
@@ -2058,7 +2058,7 @@
   int lines_per_set;
   int start = 1;
   int stop = 1;
-  int frame_lines, frame_size, title_size, seekable;
+  int frame_lines, frame_size, title_size, seekable, file_size;
   long int endoffset;
   float *binposScratch;
   FILE *fp;
@@ -2414,12 +2414,25 @@
 	fprintf(stderr, "WARNING in %s: Could not find file status for %s\n", ROUTINE, filename);
 	return NULL;
       }
+
+      // Determine Uncompressed File Size for Nframes calculation
+      file_size=0;
+      if (trajInfo->compressType==1) // Gzip
+        file_size=gzipFileSize(filename);
+      else if (trajInfo->compressType==2) // Bzip2
+        file_size=bzip2FileSize(filename);
+      else if (trajInfo->compressType==3) // Zip
+        file_size=zipFileSize(filename);
+      if (file_size<0) return NULL;
+      if (file_size==0) file_size=frame_stat.st_size;
+
       if (prnlev>0)
         fprintf(stdout,"[%i] Title offset %u   Frame Size %u    File size %lu\n",
-                worldrank,trajInfo->titleSize,trajInfo->frameSize,frame_stat.st_size);
-      if (((frame_stat.st_size - trajInfo->titleSize) % (trajInfo->frameSize)) == 0) {
+                worldrank,trajInfo->titleSize,trajInfo->frameSize,file_size);
+      trajInfo->Nframes = (int) ((file_size - trajInfo->titleSize) / trajInfo->frameSize);
+      if (((file_size - trajInfo->titleSize) % (trajInfo->frameSize)) == 0) {
 	seekable = 1;
-	stop = (int) ((frame_stat.st_size - trajInfo->titleSize) / trajInfo->frameSize);
+	stop = trajInfo->Nframes;
       } else {
 	stop = -1;
 	seekable = 0;
@@ -2538,7 +2551,8 @@
     printfone("  With this version of the code, this will likely lead to program failure!!!\n");
   }
 
-
+  // Set number of frames. Amber trajectory sets Nframes above
+  if (trajInfo->Nframes==0 && stop>0) trajInfo->Nframes=stop;
   trajInfo->start = start;
   trajInfo->stop = stop;
   trajInfo->offset = 1;
@@ -4182,7 +4196,7 @@
               fprintf(stderr,"Could not get replica temperature from file# %i\n",i);
               break;
             }
-            fprintf(stdout,"  Replica %i mytemp=%lf  ",i,repTemp);  //DEBUG 
+            if (prnlev>0) fprintf(stdout,"  Replica %i mytemp=%lf  ",i,repTemp);  //DEBUG 
             if (repTemp==currentCoordinateInfo->remdtrajtemp) {
               if (prnlev>0) fprintf(stdout,
                     "  REMD target temperature (%lf) found (%lf) at replica index %i\n",
@@ -7078,6 +7092,7 @@
   stackType *sp, *argumentStack;
   ptrajState *startingState, *currentState, **statep;
   char *continuation;
+  int totalFrames;
 
   int readCoordinates;
   int processCoordinates;
@@ -7218,18 +7233,25 @@
    */
 
   startingState->maxFrames = 0;
+  totalFrames=0;
   for (sp = transformFileStack; sp != NULL; sp = sp->next) {
     currentCoordinateInfo = (coordinateInfo *) sp->entry;
 
+    fprintf(stdout,"  %s: %i frames.\n",currentCoordinateInfo->filename,currentCoordinateInfo->Nframes);
+
     startingState->maxFrames += (currentCoordinateInfo->stop - 
 				 currentCoordinateInfo->start) /
                                  currentCoordinateInfo->offset + 1;
+    // In case we dont know how many frames will be processed, use total number of frames
+    totalFrames += currentCoordinateInfo->Nframes;
   }
 
   printfone("\nPTRAJ: Successfully read the input file.\n");
-  if (startingState->maxFrames == -1)
+  if (startingState->maxFrames == -1) {
     printfone("       Coordinate processing will occur until EOF (unknown number of frames).\n");
-  else
+    // Use total frames for action memory alloc.
+    startingState->maxFrames = totalFrames;
+  } else
     printfone("       Coordinate processing will occur on %i frames.\n", 
 	      startingState->maxFrames);
   printfone("       Summary of I/O and actions follows:\n\n");


********> bugfix 5
Author: Tyler Luchko
Date:   2010/06/25

Programs: NAB

Description:  Fixes long range asymptotics for  ionic solvents
             (e.g. NaCl in water) in 3D-RISM.  This does not affect
             calculations with pure water or other neutral solvent
             species. NAB tests are updated and added are included.

             Also improves memory handling for the Intel compiler.
             System size is no longer limited by the system stack size.


To apply the patch:
cd $AMBERHOME
patch -p0 -N < bugfix.5

---------------------------------------------------------------------------
diff --git AmberTools/src/rism/amber_rism_interface.f AmberTools/src/rism/amber_rism_interface.f
index 6847542..52feef9 100644
--- AmberTools/src/rism/amber_rism_interface.f
+++ AmberTools/src/rism/amber_rism_interface.f
@@ -501,7 +501,8 @@ subroutine rism_force (ratu_md,frc, epol, irespa)
      call timer_stop(TIME_REORIENT)
      !linproj predict
      call timer_start(TIME_CRDINTERP)
-     call fce_force(fce_o,ff,rism_3d%solu%ratu)
+     if(rismprm%apply_rism_force==1)&
+          call fce_force(fce_o,ff,rism_3d%solu%ratu)
      call timer_stop(TIME_CRDINTERP)
 
      call timer_start(TIME_REORIENT)
@@ -537,16 +538,17 @@ subroutine rism_force (ratu_md,frc, epol, irespa)
      end if
 #else /*SANDER*/
 #endif /*SANDER*/
-     call rism3d_force(rism_3d,ff)
-     if(rismprm%zerofrc==1)then
+     if(rismprm%apply_rism_force==1)then
+        call rism3d_force(rism_3d,ff)
+        if(rismprm%zerofrc==1)then
 #ifdef MPI
-        call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom,&
-             mpirank,mpisize,mpicomm)
+           call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom,&
+                mpirank,mpisize,mpicomm)
 #else
-        call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom)
+           call corr_drift(ff,rism_3d%solu%mass,rism_3d%solu%natom)
 #endif /*MPI*/
+        end if
      end if
-
      !get the excess chemical potential
      call timer_start(TIME_EXCHEM)
      if(rismprm%gauss_fluct == 0)then
@@ -563,12 +565,12 @@ subroutine rism_force (ratu_md,frc, epol, irespa)
 #endif /*defined(MPI)*/
      end if
      call timer_stop(TIME_EXCHEM)
-
+     
 #ifdef RISM_CRDINTERP
      call timer_start(TIME_REORIENT)
      call orient(rism_3d,ff,qback)
      call timer_stop(TIME_REORIENT)
-     if(rismprm%fcestride >0)then
+     if(rismprm%fcestride >0 .and. rismprm%apply_rism_force==1)then
         call timer_start(TIME_SAVECRDINTERP)
         call fce_update(fce_o,ff,rism_3d%solu%ratu)
         call timer_stop(TIME_SAVECRDINTERP)
@@ -586,7 +588,6 @@ subroutine rism_force (ratu_md,frc, epol, irespa)
 
   end if
   if(rismprm%apply_rism_force==1) frc = frc+ff
-  call flush(6)
   return
 end subroutine rism_force
 
@@ -1087,6 +1088,7 @@ end subroutine rism_writeSolvDistC
 subroutine rism_writeSolvDistF(this,step)
   use amber_rism_interface
   use rism3d_opendx
+  use safemem
   implicit none
 #if defined(MPI)
   include 'mpif.h'
@@ -1097,9 +1099,18 @@ subroutine rism_writeSolvDistF(this,step)
   character(len=16) :: cstep
   character(len=64) :: suffix
   integer :: unit = 99,iostat=0
+#ifdef MPI
+  integer :: err
+  _REAL_, pointer::work(:,:,:)=>NULL()
+#endif /*MPI*/  
 #ifdef RISM_DEBUG
   write(6,*) "printrism"
 #endif
+#ifdef MPI
+  if(len_trim(guvfile) /= 0 .or. len_trim(huvfile) /= 0)then
+     work => reallocate_pointer(work, this%ng3(1), this%ng3(2), this%nz_local)
+  end if
+#endif /*MPI*/
   !................... outputting Guv and Cuv profiles ...................
   do iv=1,this%solv%natom
      write(cstep,'(i16)') step
@@ -1112,9 +1123,15 @@ subroutine rism_writeSolvDistF(this,step)
            call mexit(6,1)
         end if
 #  if defined(MPI)
+        do k=1,this%nz_local
+           do j=1,this%ng3(2)
+              do i=1,this%ng3(1)
+                 work(i,j,k) = this%guv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2)*this%ng3(2),iv)
+              end do
+           end do
+        end do
         call writeDX(unit,&
-             (/(((this%guv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2)*this%ng3(2),iv)&
-             ,i=1,this%ng3(1)),j=1,this%ng3(2)),k=1,this%nz_local)/),&
+             work,&
              this%boxlen,this%ng3_local,this%ng3(3),this%ratucm,&
              mpirank,mpisize,mpicomm)
 #  else
@@ -1131,9 +1148,16 @@ subroutine rism_writeSolvDistF(this,step)
            call mexit(6,1)
         end if
 #  if defined(MPI)
+        
+        do k=1,this%nz_local
+           do j=1,this%ng3(2)
+              do i=1,this%ng3(1)
+                 work(i,j,k) =this%huv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2)*this%ng3(2),iv)
+              end do
+           end do
+        end do
         call writeDX(unit,&
-             (/(((this%huv(i+(j-1)*(this%ng3(1)+2)+(k-1)*(this%ng3(1)+2)*this%ng3(2),iv)&
-             ,i=1,this%ng3(1)),j=1,this%ng3(2)),k=1,this%nz_local)/),&
+             work,&
              this%boxlen,this%ng3_local,this%ng3(3),this%ratucm,&
              mpirank,mpisize,mpicomm)
 #  else
@@ -1160,6 +1184,9 @@ subroutine rism_writeSolvDistF(this,step)
         if(mpirank==0)close(unit)
      endif
   end do
+#ifdef MPI
+     err = safe_deallocate(work)
+#endif /*MPI*/
 end subroutine rism_writeSolvDistF
 
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
diff --git AmberTools/src/rism/rism3d_c.f AmberTools/src/rism/rism3d_c.f
index af51a25..ae60567 100644
--- AmberTools/src/rism/rism3d_c.f
+++ AmberTools/src/rism/rism3d_c.f
@@ -911,7 +911,7 @@ module rism3d_c
 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
     subroutine  rism3d_aexchem_sp (this,xmu0,xmu0sp,egf)
       use constants, only : PI,KB,AMBER_ELECTROSTATIC2
-      use rism_util, only : gaussquad_legendre
+      use rism_util, only : gaussquad_legendre, checksum
       implicit none
 #if defined(MPI)
       include 'mpif.h'
@@ -947,132 +947,130 @@ module rism3d_c
       call flush(6)
 #endif /*RISM_DEBUG*/
 
+      !.....total charge of solute
+      qut = sum(this%solu%charge)
       !.....getting the numerical long-range contribution
       egf = 0
-      eqkt = AMBER_ELECTROSTATIC2/KB/this%solv%temperature
-
-      Nintmx =  200
-      if(Nintmx > ntvlmx)then
-         write(6,'(1X,"Nintmx gt ntvlmx",I10)')ntvlmx
-         call mexit(6,1)
-      endif
-
-      !.....initialize gauss-legendre integration
-      call gaussquad_legendre (0d0,1d0,argum,weight,Nintmx)
-      sumhc = 0.d0
-      sumh2 = 0.d0
-
-      !.....k loop
-      do ik = 1, Nintmx
-
-         k = argum(ik)/(1.d0-argum(ik))
-
-         !.....Bessel part
-         sumb = 0.d0
-
-         do i=2,this%solu%natom
-            do j=1,i-1
-
-               !......... site separation  ..........
-               dx = this%solu%ratu(1,i) - this%solu%ratu(1,j)
-               dy = this%solu%ratu(2,i) - this%solu%ratu(2,j)
-               dz = this%solu%ratu(3,i) - this%solu%ratu(3,j)
-
-               r2 = dx*dx + dy*dy + dz*dz
-
-               xarg = this%solv%xappa*k*sqrt(r2)
-               if(xarg == 0.d0) &
-                    sumb = sumb + 1.d0*this%solu%charge(i)*this%solu%charge(j)
-               if(xarg /= 0.d0) &
-                    sumb = sumb + sin(xarg)/xarg *this%solu%charge(i)*this%solu%charge(j)
 
+      if(this%mpirank==0)then         
+         eqkt = AMBER_ELECTROSTATIC2/KB/this%solv%temperature
+         Nintmx =  200
+         if(Nintmx > ntvlmx)then
+            write(6,'(1X,"Nintmx gt ntvlmx",I10)')ntvlmx
+            call mexit(6,1)
+         endif
+         
+         !.....initialize gauss-legendre integration
+         call gaussquad_legendre (0d0,1d0,argum,weight,Nintmx)
+         sumhc = 0.d0
+         sumh2 = 0.d0
+         
+         !.....k loop
+         do ik = 1, Nintmx
+            
+            k = argum(ik)/(1.d0-argum(ik))
+            
+            !.....Bessel part
+            sumb = 0.d0
+            
+            do i=2,this%solu%natom
+               do j=1,i-1
+                  
+                  !......... site separation  ..........
+                  dx = this%solu%ratu(1,i) - this%solu%ratu(1,j)
+                  dy = this%solu%ratu(2,i) - this%solu%ratu(2,j)
+                  dz = this%solu%ratu(3,i) - this%solu%ratu(3,j)
+                  
+                  r2 = dx*dx + dy*dy + dz*dz
+                  
+                  xarg = this%solv%xappa*k*sqrt(r2)
+                  if(xarg == 0.d0) &
+                       sumb = sumb + 1.d0*this%solu%charge(i)*this%solu%charge(j)
+                  if(xarg /= 0.d0) &
+                       sumb = sumb + sin(xarg)/xarg *this%solu%charge(i)*this%solu%charge(j)
+                  
+               enddo
             enddo
+            
+            sumb = sumb*2.d0
+            
+            do i=1,this%solu%natom
+               sumb = sumb + 1.d0*this%solu%charge(i)*this%solu%charge(i)
+            enddo
+            
+            !.....end of Bessel part
+            
+            x2arg = (k*this%solv%xappa*this%solv%smear)**2
+            k2 = k**2
+            
+            denom = argum(ik)**2+(1.0d0-argum(ik))**2
+            
+            sumhc = sumhc + &
+                 exp(-x2arg/2.d0)/denom*sumb*weight(ik)
+            sumh2 = sumh2 + &
+                 exp(-x2arg/2.d0)*argum(ik)**2/(denom**2)*sumb*weight(ik)
+            
          enddo
-
-         sumb = sumb*2.d0
-
-         do i=1,this%solu%natom
-            sumb = sumb + 1.d0*this%solu%charge(i)*this%solu%charge(i)
-         enddo
-
-         !.....end of Bessel part
-
-         x2arg = (k*this%solv%xappa*this%solv%smear)**2
-         k2 = k**2
-
-         denom = argum(ik)**2+(1.0d0-argum(ik))**2
-
-         sumhc = sumhc + &
-              exp(-x2arg/2.d0)/denom*sumb*weight(ik)
-         sumh2 = sumh2 + &
-              exp(-x2arg/2.d0)*argum(ik)**2/(denom**2)*sumb*weight(ik)
-
-      enddo
-
-      !.....end of k-loop
-
-      !.....total charge of solute
-      qut = 0.d0
-      do i = 1,this%solu%natom
-         qut = qut + this%solu%charge(i)
-      enddo
-      !.....site xappa
-      if (this%closure == KH)  then
+         
+         !.....end of k-loop
+         
+         !.....site xappa
+         if (this%closure == KH)  then
+            do iv = 1,this%solv%natom
+               if(qut*this%solv%charge_sp(iv) <= 0.d0) &
+                    xmuh2lr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge_sp(iv)**2
+               if(qut*this%solv%charge_sp(iv) > 0.d0) &
+                    xmuh2lr(iv) = 0.d0
+               xmuhclr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv)
+            enddo
+         else
+            do iv = 1,this%solv%natom
+               xmuh2lr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge_sp(iv)**2
+               xmuhclr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv)
+            enddo
+         endif
+         
+         !.....unit for xappa
          do iv = 1,this%solv%natom
-            if(qut*this%solv%charge_sp(iv) <= 0.d0) &
-                 xmuh2lr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge_sp(iv)**2
-            if(qut*this%solv%charge_sp(iv) > 0.d0) &
-                 xmuh2lr(iv) = 0.d0
-            xmuhclr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv)
+            xmuh2lr(iv) = xmuh2lr(iv) * eqkt
+            xmuhclr(iv) = xmuhclr(iv) * eqkt
          enddo
-      else
+         
+         !.....divided by total xappa
+         if(this%solv%xappa /= 0.d0)then
+            do iv = 1,this%solv%natom
+               xmuh2lr(iv) = xmuh2lr(iv) / this%solv%xappa
+               xmuhclr(iv) = xmuhclr(iv) / this%solv%xappa
+            enddo
+         else
+            do iv = 1,this%solv%natom
+               xmuh2lr(iv) = 0.d0
+               xmuhclr(iv) = 0.d0
+            enddo
+         endif
+         
+         !.....multiplying xmulr by integral
          do iv = 1,this%solv%natom
-            xmuh2lr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge_sp(iv)**2
-            xmuhclr(iv) = 4.d0*PI/(this%solv%dielconst) * this%solv%rho(iv)*this%solv%charge(iv)*this%solv%charge_sp(iv)
+            xmuh2lr(iv) =   xmuh2lr(iv)*sumh2
+            xmuhclr(iv) = - xmuhclr(iv)*sumhc
          enddo
-      endif
-
-      !.....unit for xappa
-      do iv = 1,this%solv%natom
-         xmuh2lr(iv) = xmuh2lr(iv) * eqkt
-         xmuhclr(iv) = xmuhclr(iv) * eqkt
-      enddo
-
-      !.....divided by total xappa
-      if(this%solv%xappa /= 0.d0)then
+         
+         sumh2 = 0.d0
+         sumhc = 0.d0
          do iv = 1,this%solv%natom
-            xmuh2lr(iv) = xmuh2lr(iv) / this%solv%xappa
-            xmuhclr(iv) = xmuhclr(iv) / this%solv%xappa
+            sumh2 = sumh2 + xmuh2lr(iv)
+            sumhc = sumhc + xmuhclr(iv)
          enddo
-      else
+         
+         !.....J devided by KT
+         sumh2 = sumh2 / (PI*this%solv%dielconst) * eqkt
+         sumhc = sumhc / PI * eqkt
          do iv = 1,this%solv%natom
-            xmuh2lr(iv) = 0.d0
-            xmuhclr(iv) = 0.d0
+            xmuh2lr(iv) = xmuh2lr(iv) / (PI*this%solv%dielconst) * eqkt
+            xmuhclr(iv) = xmuhclr(iv) / PI * eqkt
          enddo
-      endif
-
-      !.....multiplying xmulr by integral
-      do iv = 1,this%solv%natom
-         xmuh2lr(iv) =   xmuh2lr(iv)*sumh2
-         xmuhclr(iv) = - xmuhclr(iv)*sumhc
-      enddo
-
-      sumh2 = 0.d0
-      sumhc = 0.d0
-      do iv = 1,this%solv%natom
-         sumh2 = sumh2 + xmuh2lr(iv)
-         sumhc = sumhc + xmuhclr(iv)
-      enddo
-
-      !.....J devided by KT
-      sumh2 = sumh2 / (PI*this%solv%dielconst) * eqkt
-      sumhc = sumhc / PI * eqkt
-      do iv = 1,this%solv%natom
-         xmuh2lr(iv) = xmuh2lr(iv) / (PI*this%solv%dielconst) * eqkt
-         xmuhclr(iv) = xmuhclr(iv) / PI * eqkt
-      enddo
-      xmulr = sumh2 + sumhc
-
+         xmulr = sumh2 + sumhc
+      end if
       !.................. calculating xMu0 by PLHNC closure ..................
       if (this%closure == KH)  then
          dxmu = 0.d0
@@ -1232,13 +1230,20 @@ module rism3d_c
          xmu0sp(iv) = xmu0sp(iv) * (this%boxvol/this%ngr)
       enddo
 
-      !.....add long-range part
-      xmu0 = xmu0 + (xmulr)
-      egf = egf + (xmulr)
-      do iv=1,this%solv%natom
-         xmu0sp(iv) = xmu0sp(iv) + xmuh2lr(iv) + xmuhclr(iv)
-      enddo
-
+      !.....add long-range part but only on the master process so we don't over count
+      !.....this contribution.
+!!$      write(0,*) "pre lr", this%mpirank, xmu0
+!!$      write(0,*) checksum(this%huv,product(shape(this%huv)),this%mpicomm), &
+!!$           checksum(this%cuv,product(shape(this%cuv)),this%mpicomm), &
+!!$           checksum(this%uuv,product(shape(this%uuv)),this%mpicomm)
+      if(this%mpirank==0)then
+         xmu0 = xmu0 + (xmulr)
+         egf = egf + (xmulr)
+         do iv=1,this%solv%natom
+            xmu0sp(iv) = xmu0sp(iv) + xmuh2lr(iv) + xmuhclr(iv)
+         enddo
+      end if
+!!$      write(0,*) "post lr", this%mpirank, xmu0
       return
     end subroutine rism3d_aexchem_sp
 
@@ -2322,6 +2327,7 @@ end subroutine reallocbox
   subroutine  asympch(this,huvk0)
       use constants, only : PI, FOURPI,&
            AMBER_ELECTROSTATIC2,KB
+      use rism_util, only : checksum
       implicit none
 #if defined(MPI)
       include 'mpif.h'
@@ -2339,9 +2345,7 @@ end subroutine reallocbox
       _REAL_ :: xappa2,smear2_4
       _REAL_ :: asymhr_coeff
       _REAL_,save :: asymhr_coeff_at_cut=0,asymcr_coeff_at_cut=0
-      _REAL_,save :: erfcAtCut=0,erfcAtNegCut=0,cut=15.5d0
-!!      _REAL_,save :: erfcAtCut=0,erfcAtNegCut=0,cut=999d0
-!      !linear spacing of the grid
+      _REAL_,save :: erfcAtCut=0,erfcAtNegCut=0,cut=4d0,maxcut
       !offset :: z-axis offset (important for spatially distributed MPI)
       _REAL_ :: offset
 !      !number of gridpoints in each direction to use
@@ -2351,7 +2355,7 @@ end subroutine reallocbox
       _REAL_ ::      erfc
       external  erfc
       integer :: irank,ierr,i
-      _REAL_:: checksum,mpitmp
+      _REAL_:: mpitmp
 
       half_smear_root_pi=sqrt(PI)*this%solv%smear/2d0
       half_xappa_smear=this%solv%xappa*this%solv%smear/2d0
@@ -2361,7 +2365,9 @@ end subroutine reallocbox
       asymhr_coeff=exp(-(this%solv%xappa**2)*(this%solv%smear**2)/4d0)* &
            (2d0*exp(-(this%solv%smear*this%solv%xappa/2d0)**2)/(sqrt(PI)*this%solv%smear) &
            - this%solv%xappa * erfc(this%solv%xappa*this%solv%smear/2d0))
-      do while(exp(-quarter_xappa2_smear2)-asymhr_coeff_at_cut > 1d-7 .and. 1d0-asymcr_coeff_at_cut > 1d-7)
+      maxcut = sqrt(sum(this%boxlen**2))
+      do while((exp(-quarter_xappa2_smear2)-asymhr_coeff_at_cut > 1d-7 .or. 1d0-asymcr_coeff_at_cut > 1d-7)&
+           .and. cut < maxcut)
          erfcAtCut = erfc(cut)
          erfcAtNegCut = erfc(-cut)
          asymhr_coeff_at_cut=exp(-quarter_xappa2_smear2) &
@@ -2370,10 +2376,10 @@ end subroutine reallocbox
          !(erfcAtNegCut - erfcAtCut)/2d0
          asymcr_coeff_at_cut=(1d0-erfc(cut/this%solv%smear))
          cut = cut+.1d0
-         !      write(6,*)'cut coeff',asymhr_coeff_at_cut,asymcr_coeff_at_cut
+!         write(0,*)'cut coeff',this%mpirank,asymhr_coeff_at_cut,asymcr_coeff_at_cut
       end do
 #ifdef RISM_DEBUG
-      write(6,*)'cut coeff',cut,asymhr_coeff_at_cut,asymcr_coeff_at_cut
+      write(0,*)'cut coeff',cut,exp(-quarter_xappa2_smear2)-asymhr_coeff_at_cut,asymcr_coeff_at_cut
 #endif  /*RISM_DEBUG*/
       !.....initialize
       this%asymcr=0d0
@@ -2569,7 +2575,7 @@ end subroutine reallocbox
       this%asymcr = this%asymcr * factor
       this%asymhr = this%asymhr * factor
       this%asymck = this%asymck * (factor / this%boxvol)
-      this%asymhk = this%asymhk * (factor / this%boxvol)/2d0/PI**2
+      this%asymhk = this%asymhk * (factor / this%boxvol)
 
       !?WHY IS THIS ONLY FOR ny_start==0?!
       if(this%ny_start==0)then
@@ -2591,35 +2597,22 @@ end subroutine reallocbox
       end if
 #ifdef RISM_DEBUG
 #  ifdef MPI    
-    checksum = sum(this%asymck)
-#      ifdef USE_MPI_IN_PLACE
-    call mpi_allreduce(MPI_IN_PLACE,checksum,1,MPI_DOUBLE_PRECISION,mpi_sum,this%mpicomm,ierr)
-#      else
-    call mpi_allreduce(checksum,mpitmp,1,MPI_DOUBLE_PRECISION,mpi_sum,this%mpicomm,ierr)
-    checksum = mpitmp
-#      endif /*USE_MPI_IN_PLACE*/
-    if(this%mpirank == 0)then
-       write(6,*) "SUM this%asymck", this%mpirank, checksum
-       call flush(6)
-    end if
-    checksum = sum(this%asymhk)
-#      ifdef USE_MPI_IN_PLACE
-    call mpi_allreduce(MPI_IN_PLACE,checksum,1,MPI_DOUBLE_PRECISION,mpi_sum,this%mpicomm,ierr)
-#      else
-    call mpi_allreduce(checksum,mpitmp,1,MPI_DOUBLE_PRECISION,mpi_sum,this%mpicomm,ierr)
-    checksum = mpitmp
-#      endif /*USE_MPI_IN_PLACE*/
-    if(this%mpirank == 0)then
-       write(6,*) "SUM this%asymhk", this%mpirank, checksum
+       write(6,*) "SUM this%asymhr", this%mpirank, &
+            checksum(this%asymhr,product(shape(this%asymhr)), this%mpicomm), sum(this%asymhr)
+       write(6,*) "SUM this%asymcr", this%mpirank, &
+            checksum(this%asymcr,product(shape(this%asymcr)), this%mpicomm), sum(this%asymcr)
        call flush(6)
-    end if
 #  else
-         write(6,*)"SUM this%asymcr ",size(this%asymcr),sum(this%asymcr),&
-              sum(this%asymcr(1:this%ngr_local/2)),sum(this%asymcr(this%ngr_local/2+1:this%ngr_local))
-         write(6,*)"SUM this%asymhr ",size(this%asymhr),sum(this%asymhr),&
-              sum(this%asymhr(1:this%ngr_local/2)),sum(this%asymhr(this%ngr_local/2+1:this%ngr_local))
+    write(6,*) cut, asymhr_coeff_at_cut, asymcr_coeff_at_cut
+    write(6,*)"SUM this%asymcr ",size(this%asymcr),sum(this%asymcr),&
+         sum(this%asymcr(1:this%ngr_local/2)),sum(this%asymcr(this%ngr_local/2+1:this%ngr_local))
+    write(6,*)"SUM this%asymhr ",size(this%asymhr),sum(this%asymhr),&
+         sum(this%asymhr(1:this%ngr_local/2)),sum(this%asymhr(this%ngr_local/2+1:this%ngr_local))
+    stop
+#  endif /*MPI    */
 #endif /*RISM_DEBUG*/
 #ifdef RISM_DEBUG
+#  ifdef MPI    
       write(6,*) "RANK",this%mpirank,factor,this%boxvol
       write(6,'(a,i4,f15.10,f15.10)') "SUM this%asymck",this%ngk,sum(this%asymck),sum(this%asymck(3:))
       write(6,'(a,i4,f15.10,f15.10)') "SUM this%asymhk",this%ngk,sum(this%asymhk),sum(this%asymhk(3:))
diff --git AmberTools/src/rism/rism3d_opendx.f AmberTools/src/rism/rism3d_opendx.f
index c2f6dca..97a22f6 100644
--- AmberTools/src/rism/rism3d_opendx.f
+++ AmberTools/src/rism/rism3d_opendx.f
@@ -55,28 +55,37 @@ module rism3d_opendx
 contains
   subroutine writeDX (unit, data, rism_box, n,nz_total,ratucm &
 #ifdef MPI
-       ,rank,size,comm &
+       ,rank,nproc,comm &
 #endif /*MPI*/
 ) 
+    use safemem
     implicit none
 #if defined(MPI)
     include 'mpif.h'
-    integer, intent(in) ::  rank,size,comm
+    integer, intent(in) ::  rank,nproc,comm
 #else
-    integer,parameter :: rank = 0, size=1
+    integer,parameter :: rank = 0, nproc=1
 #endif /*defined(MPI)*/
     integer, intent(in) :: nz_total
     integer,intent(in) :: unit, n(3)
     _REAL_,intent(in) :: data(n(1),n(2),n(3)), rism_box(3),ratucm(3)
     integer :: i,j,k, irank, ierr,count,icount
-    integer :: nz_offset(size),nz_local(size)
+    integer :: nz_offset(nproc),nz_local(nproc)
     integer, parameter :: dataperline=3
-    _REAL_ :: z_data(nz_total)
+#ifdef MPI
+    integer :: err
+    _REAL_,pointer :: z_data(:)=>NULL()
+#endif /*MPI*/
 #ifdef RISM_DEBUG
+
     write(6,*) "writeDX",rism_box,ratucm
     call flush(6)
 #endif /*RISM_DEBUG*/
-
+!!$    do i = 1,nproc
+!!$       if(rank==i)&
+!!$            write(0,*) "DX",rank,sum(data)/(rank+1),n(3)
+!!$       call mpi_barrier(comm,ierr)
+!!$    end do
     if(rank==0)then
        write(unit,"(a,i8,i8,i8)") "object 1 class gridpositions counts",n(1),n(2),nz_total
        write(unit,"(a,3(f15.8))") "origin ",ratucm(1)-rism_box(1)/2,ratucm(2)-rism_box(2)/2,ratucm(3)-rism_box(3)/2
@@ -89,9 +98,14 @@ contains
     end if
     count = 0
 #if defined(MPI)
+    z_data =>reallocate_pointer(z_data,nz_total)
     call mpi_gather(n(3),1,mpi_integer,nz_local,1,mpi_integer,0,comm,ierr)
     nz_offset(1) = 0
-    nz_offset(2:) = nz_local(1:size-1)
+    do i = 2, nproc
+       nz_offset(i) =sum( nz_local(1:i-1))
+    end do
+!!$    if(rank==0)&
+!!$         write(0,*) "NZ",rank,nz_offset, nz_local
 #endif /*defined(MPI)*/
     do i=1,n(1)
        do j=1,n(2)
@@ -122,5 +136,8 @@ contains
        end if
        write(unit,"(a)") 'object "Untitled" call field'
     end if
+#ifdef MPI
+    err = safe_deallocate(z_data)
+#endif /*MPI*/
   end subroutine writeDX
 end module rism3d_opendx
diff --git AmberTools/src/rism/rism_fft.f AmberTools/src/rism/rism_fft.f
index 75ef461..72779e3 100644
--- AmberTools/src/rism/rism_fft.f
+++ AmberTools/src/rism/rism_fft.f
@@ -205,19 +205,23 @@ contains
     ! Normalizing while Forward FFT (KEY=1)                  *
     !***********************************************************************
     subroutine  rlft3i (data, ng3, key,n_local,plan)
+      use safemem
       implicit none
       integer ::  ng3(3), key
       integer :: n_local
       integer*8,intent(in) :: plan
-      _REAL_ ::  data((ng3(1)+2)*ng3(2)*n_local)
-      _REAL_ :: work((ng3(1)+2)*ng3(2)*n_local)
+!      _REAL_ ::  data((ng3(1)+2)*ng3(2)*n_local)
+!      _REAL_ :: work((ng3(1)+2)*ng3(2)*n_local)
+      _REAL_ ::  data(:)
+      _REAL_,pointer :: work(:)
       integer ::  ngr, ngr_local,ngk_local, ig, ierr
       integer, parameter :: FFTW_TRANSPOSED_ORDER=1, FFTW_NORMAL_ORDER=0
       !....................... R-space data array size .......................
 #  ifdef RISM_DEBUG
-      write(6,*) "rlft3i",n_local
-      call flush(6)
+      write(0,*) "rlft3i",n_local
+      call flush(0)
 #  endif /*RISM_DEBUG*/
+      work=>reallocate_pointer(work,size(data))
       ngr = ng3(1)*ng3(2)*ng3(3)
       ngr_local = ng3(1)*ng3(2)*n_local
       ngk_local = (ng3(1)+2)*ng3(2)*n_local
@@ -230,6 +234,7 @@ contains
          call rfftwnd_f77_mpi( plan,1,data,work,1,                    &
               FFTW_TRANSPOSED_ORDER)
       end if
+      ierr = safe_deallocate(work)
     end subroutine rlft3i
 
 #else /*defined(MPI)*/
diff --git AmberTools/test/nab/Makefile AmberTools/test/nab/Makefile
index 2c8ba0f..225aa66 100644
--- AmberTools/test/nab/Makefile
+++ AmberTools/test/nab/Makefile
@@ -12,7 +12,7 @@ testlibrism: duplex_test deform_test reflexive_test hashed_test shifts_test \
 	rattle_md_test rembed_test dhfrndpmtx_test asp_test \
 	aspnb_test prm_test cif_test xmin_test \
 	lmod_test nmode1_test nmode2_test nmode3_test ips_test \
-	pbsa_test rism_test rism_md_test rism_dist rism_hnc
+	pbsa_test rism_test rism_md_test rism_dist rism_hnc rism_ion
 
 duplex_test::
 	@./Run.duplex
@@ -112,3 +112,6 @@ rism_hnc::
 
 rism_dist::
 	@./Run.rism_dist
+
+rism_ion::
+	@sh ./Run.rism_ion
diff --git AmberTools/test/nab/Na+.parm7 AmberTools/test/nab/Na+.parm7
new file mode 100644
index 0000000..f7b5a1f
--- /dev/null
+++ AmberTools/test/nab/Na+.parm7
@@ -0,0 +1,124 @@
+%VERSION  VERSION_STAMP = V0001.000  DATE = 06/20/07  15:21:17                  
+%FLAG TITLE                                                                     
+%FORMAT(20a4)                                                                   
+                                                                                
+%FLAG POINTERS                                                                  
+%FORMAT(10I8)                                                                   
+       1       1       0       0       0       0       0       0       0       0
+       1       1       0       0       0       0       0       0       1       0
+       0       0       0       0       0       0       0       1       1       0
+       0
+%FLAG ATOM_NAME                                                                 
+%FORMAT(20a4)                                                                   
+Na+ 
+%FLAG CHARGE                                                                    
+%FORMAT(5E16.8)                                                                 
+  1.82223000E+01
+%FLAG MASS                                                                      
+%FORMAT(5E16.8)                                                                 
+  2.29900000E+01
+%FLAG ATOM_TYPE_INDEX                                                           
+%FORMAT(10I8)                                                                   
+       1
+%FLAG NUMBER_EXCLUDED_ATOMS                                                     
+%FORMAT(10I8)                                                                   
+       1
+%FLAG NONBONDED_PARM_INDEX                                                      
+%FORMAT(10I8)                                                                   
+       1
+%FLAG RESIDUE_LABEL                                                             
+%FORMAT(20a4)                                                                   
+Na+ 
+%FLAG RESIDUE_POINTER                                                           
+%FORMAT(10I8)                                                                   
+       1
+%FLAG BOND_FORCE_CONSTANT                                                       
+%FORMAT(5E16.8)                                                                 
+
+%FLAG BOND_EQUIL_VALUE                                                          
+%FORMAT(5E16.8)                                                                 
+
+%FLAG ANGLE_FORCE_CONSTANT                                                      
+%FORMAT(5E16.8)                                                                 
+
+%FLAG ANGLE_EQUIL_VALUE                                                         
+%FORMAT(5E16.8)                                                                 
+
+%FLAG DIHEDRAL_FORCE_CONSTANT                                                   
+%FORMAT(5E16.8)                                                                 
+
+%FLAG DIHEDRAL_PERIODICITY                                                      
+%FORMAT(5E16.8)                                                                 
+
+%FLAG DIHEDRAL_PHASE                                                            
+%FORMAT(5E16.8)                                                                 
+
+%FLAG SOLTY                                                                     
+%FORMAT(5E16.8)                                                                 
+  0.00000000E+00
+%FLAG LENNARD_JONES_ACOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  2.04815198E+04
+%FLAG LENNARD_JONES_BCOEF                                                       
+%FORMAT(5E16.8)                                                                 
+  1.50643699E+01
+%FLAG BONDS_INC_HYDROGEN                                                        
+%FORMAT(10I8)                                                                   
+
+%FLAG BONDS_WITHOUT_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
+
+%FLAG ANGLES_INC_HYDROGEN                                                       
+%FORMAT(10I8)                                                                   
+
+%FLAG ANGLES_WITHOUT_HYDROGEN                                                   
+%FORMAT(10I8)                                                                   
+
+%FLAG DIHEDRALS_INC_HYDROGEN                                                    
+%FORMAT(10I8)                                                                   
+
+%FLAG DIHEDRALS_WITHOUT_HYDROGEN                                                
+%FORMAT(10I8)                                                                   
+
+%FLAG EXCLUDED_ATOMS_LIST                                                       
+%FORMAT(10I8)                                                                   
+       0
+%FLAG HBOND_ACOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBOND_BCOEF                                                               
+%FORMAT(5E16.8)                                                                 
+
+%FLAG HBCUT                                                                     
+%FORMAT(5E16.8)                                                                 
+
+%FLAG AMBER_ATOM_TYPE                                                           
+%FORMAT(20a4)                                                                   
+IP  
+%FLAG TREE_CHAIN_CLASSIFICATION                                                 
+%FORMAT(20a4)                                                                   
+M   
+%FLAG JOIN_ARRAY                                                                
+%FORMAT(10I8)                                                                   
+       0
+%FLAG IROTAT                                                                    
+%FORMAT(10I8)                                                                   
+       0
+%FLAG SOLVENT_POINTERS                                                          
+%FORMAT(3I8)                                                                    
+       1       1       2
+%FLAG ATOMS_PER_MOLECULE                                                        
+%FORMAT(10I8)                                                                   
+       1
+%FLAG BOX_DIMENSIONS                                                            
+%FORMAT(5E16.8)                                                                 
+  9.00000000E+01  2.56000000E+01  2.56000000E+01  2.56000000E+01
+%FLAG RADIUS_SET                                                                
+%FORMAT(1a80)                                                                   
+modified Bondi radii (mbondi)                                                   
+%FLAG RADII                                                                     
+%FORMAT(5E16.8)                                                                 
+  1.50000000E+00
+%FLAG SCREEN                                                                    
+%FORMAT(5E16.8)                                                                 
+  8.00000000E-01
diff --git AmberTools/test/nab/Na+.pdb AmberTools/test/nab/Na+.pdb
new file mode 100644
index 0000000..bb701f8
--- /dev/null
+++ AmberTools/test/nab/Na+.pdb
@@ -0,0 +1,4 @@
+REMARK                                                              
+ATOM      1 Na+  Na+     1       0.000   0.000   0.000  1.00  0.00           N  
+TER   
+END   
diff --git AmberTools/test/nab/Run.rism_ion AmberTools/test/nab/Run.rism_ion
new file mode 100755
index 0000000..7aaec66
--- /dev/null
+++ AmberTools/test/nab/Run.rism_ion
@@ -0,0 +1,39 @@
+#!/bin/sh
+
+toomany() {
+    echo "${0}: This test requires 1, 2, 3, 4, 6, 8, 12 or 24 processes"
+    echo "for meaningful comparison."
+    exit 0
+}
+
+if [ -n "${DO_PARALLEL}" ] ; then
+    numprocs=`echo $DO_PARALLEL | awk -f ../numprocs.awk `
+    if [ ! \( "$numprocs" -eq "12" -o "$numprocs" -eq "24"\
+        -o "$numprocs" -eq "8" -o "$numprocs" -eq "6"\
+        -o "$numprocs" -eq "3" -o "$numprocs" -eq "4"\
+        -o "$numprocs" -eq "2" -o "$numprocs" -le "1" \) ]; then
+            echo " DO_PARALLEL set to $DO_PARALLEL"
+            toomany 
+    elif [ -n "${MP_PROCS}" ]; then
+        if [  ! \( "$MP_PROCS" -eq "12" -o "$MP_PROCS" -eq "24"\
+            -o "$MP_PROCS" -eq "8" -o "$MP_PROCS" -eq "6"\
+            -o "$MP_PROCS" -eq "3" -o "$MP_PROCS" -eq "4"\
+            -o "$MP_PROCS" -eq "2" -o "$MP_PROCS" -le "1" \) ]; then
+#               --- For IBM AIX ---
+            echo "    MP_PROCS set to "$MP_PROCS
+            toomany 
+        fi
+    fi
+fi
+. ../program_error.sh
+
+echo "Running test for ionic solvent and charge solute"
+echo "(this tests the 3D-RISM-KH implementation)"
+echo ""
+../../bin/nab -o sff rismion.nab || error
+$DO_PARALLEL ./sff > rismion.out || error
+
+../dacdif rismion.out.check rismion.out
+
+rm -f sff rismion.c
+exit 0
diff --git AmberTools/test/nab/cuv.H1.4.dx.check AmberTools/test/nab/cuv.H1.4.dx.check
index a53e547..0da490c 100644
--- AmberTools/test/nab/cuv.H1.4.dx.check
+++ AmberTools/test/nab/cuv.H1.4.dx.check
@@ -344,7 +344,7 @@ object 3 class array type double rank 0 items     5184 follows
     0.70282E-001    0.80739E-001    0.91198E-001
     0.94417E-001    0.91703E-001    0.77197E-001
     0.50502E-001    0.19853E-001   -0.36599E-003
-    0.22738E-005    0.16691E-001    0.36195E-001
+    0.22736E-005    0.16691E-001    0.36195E-001
     0.49401E-001    0.53981E-001    0.53966E-001
     0.47335E-001    0.56527E-001    0.67703E-001
     0.78860E-001    0.90368E-001    0.10008E+000
diff --git AmberTools/test/nab/huv.H1.4.dx.check AmberTools/test/nab/huv.H1.4.dx.check
index 50eb343..dcd2990 100644
--- AmberTools/test/nab/huv.H1.4.dx.check
+++ AmberTools/test/nab/huv.H1.4.dx.check
@@ -37,7 +37,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.39322E-002   -0.18784E-002   -0.58137E-002
     0.10207E-002    0.62249E-003   -0.98638E-003
     0.37094E-003   -0.28752E-003    0.22042E-004
-   -0.99891E-004    0.15368E-003   -0.19634E-004
+   -0.99891E-004    0.15368E-003   -0.19635E-004
     0.35824E-003   -0.40488E-003    0.40397E-003
     0.14213E-003    0.61945E-002   -0.76858E-002
     0.81862E-002   -0.54091E-002    0.13352E-002
@@ -58,7 +58,7 @@ object 3 class array type double rank 0 items     5184 follows
     0.22994E-002   -0.34751E-002   -0.37733E-001
    -0.16433E-001   -0.59317E-002    0.71093E-002
    -0.46373E-002    0.32238E-002   -0.25894E-002
-    0.22145E-002   -0.65291E-004   -0.12695E-003
+    0.22145E-002   -0.65292E-004   -0.12695E-003
    -0.16873E-003    0.45506E-003   -0.14159E-002
     0.16342E-002   -0.79582E-002    0.56556E-002
    -0.43786E-001   -0.46923E-002   -0.27685E-002
@@ -96,11 +96,11 @@ object 3 class array type double rank 0 items     5184 follows
     0.34445E-003    0.33513E-002    0.63723E-003
    -0.45516E-003    0.16641E-004   -0.90223E-004
     0.10300E-003   -0.99252E-004    0.15249E-004
-   -0.10662E-004   -0.19945E-004   -0.63404E-006
+   -0.10662E-004   -0.19945E-004   -0.63406E-006
     0.11124E-004   -0.28230E-004   -0.31534E-003
    -0.33642E-002   -0.57217E-003   -0.27793E-002
    -0.74846E-003    0.29526E-003   -0.94696E-004
-    0.64217E-004   -0.66025E-004   -0.40449E-005
+    0.64216E-004   -0.66025E-004   -0.40449E-005
    -0.30799E-004   -0.16361E-004   -0.62269E-004
    -0.51020E-005   -0.16001E-003    0.92448E-004
    -0.57830E-003   -0.21012E-002   -0.69590E-003
@@ -117,7 +117,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.21378E-002   -0.44258E-003   -0.15111E-002
    -0.13934E-002    0.53131E-003   -0.22947E-003
    -0.74937E-005   -0.46655E-004   -0.61371E-004
-    0.61593E-004    0.13955E-004    0.16010E-003
+    0.61594E-004    0.13955E-004    0.16010E-003
    -0.17966E-003    0.34275E-003   -0.36108E-003
     0.76113E-003    0.23418E-002    0.29182E-003
     0.19046E-002    0.12879E-002   -0.85274E-003
@@ -131,7 +131,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.24936E-003    0.43593E-003   -0.38975E-003
     0.48502E-003   -0.28550E-003    0.94466E-003
     0.27789E-002    0.71808E-003    0.38223E-002
-   -0.14124E-004   -0.13567E-002    0.12326E-002
+   -0.14125E-004   -0.13567E-002    0.12326E-002
    -0.66934E-003    0.45864E-003   -0.28062E-003
    -0.43706E-003    0.34374E-003   -0.56160E-003
     0.23427E-003   -0.19776E-003   -0.12917E-003
@@ -182,7 +182,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.11703E-002    0.14706E-002   -0.40144E-003
     0.10286E-003    0.45475E-004   -0.49081E-004
    -0.47357E-004    0.54489E-006   -0.61082E-004
-    0.65984E-004   -0.69587E-004   -0.10541E-003
+    0.65984E-004   -0.69588E-004   -0.10541E-003
     0.64247E-003    0.25698E-002    0.28005E-002
     0.27413E-002    0.12876E-002   -0.75471E-003
     0.57492E-004    0.66448E-004   -0.42928E-004
@@ -229,7 +229,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.40783E-002    0.30972E-002   -0.35632E-002
    -0.14974E-004    0.13258E-002   -0.10864E-002
     0.34485E-003   -0.16911E-003   -0.62126E-004
-    0.72158E-004   -0.22208E-004    0.77266E-004
+    0.72158E-004   -0.22208E-004    0.77265E-004
     0.24040E-003   -0.72533E-003    0.13593E-002
    -0.16119E-002    0.10078E-001   -0.20050E-001
     0.72175E-002   -0.45419E-002    0.45478E-003
@@ -292,7 +292,7 @@ object 3 class array type double rank 0 items     5184 follows
     0.33230E-003   -0.62327E-003    0.36713E-003
    -0.30819E-002   -0.32037E-003   -0.17162E-002
    -0.14580E-002    0.46999E-003   -0.97290E-004
-   -0.73333E-004    0.14729E-006   -0.11485E-003
+   -0.73333E-004    0.14727E-006   -0.11485E-003
    -0.10058E-003    0.62528E-004   -0.17489E-003
     0.15221E-003   -0.46879E-003    0.25396E-003
    -0.52915E-003   -0.27851E-002    0.22929E-002
@@ -318,7 +318,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.68610E-003    0.64051E-003   -0.81356E-003
     0.24281E-003   -0.94464E-003   -0.31260E-002
     0.48815E-002   -0.32512E-002   -0.12194E-002
-    0.15282E-002   -0.10747E-002    0.37017E-003
+    0.15282E-002   -0.10747E-002    0.37016E-003
    -0.43401E-003    0.37194E-003    0.90390E-003
    -0.87376E-003    0.10045E-002   -0.10100E-002
     0.89048E-003   -0.53634E-003    0.18096E-002
@@ -355,14 +355,14 @@ object 3 class array type double rank 0 items     5184 follows
     0.26923E-003   -0.62333E-003    0.92867E-003
    -0.23947E-002    0.40142E-002   -0.86299E-002
     0.45605E-002   -0.33767E-001    0.48411E-002
-   -0.86790E-002    0.13146E-002   -0.92538E-004
+   -0.86790E-002    0.13146E-002   -0.92539E-004
    -0.33552E-003   -0.15197E-003    0.54828E-004
    -0.61954E-003    0.61334E-003   -0.71350E-003
     0.88754E-003   -0.46185E-003   -0.11825E-002
     0.49261E-002   -0.92336E-002    0.11674E-001
    -0.57510E-002    0.61122E-002    0.39077E-003
    -0.16127E-002    0.13002E-002   -0.76188E-003
-    0.68127E-003    0.46393E-003   -0.60936E-003
+    0.68127E-003    0.46394E-003   -0.60936E-003
     0.83803E-003   -0.13684E-002    0.18949E-002
    -0.20507E-002    0.86720E-003    0.55761E-002
    -0.38872E-002    0.87045E-002    0.57034E-003
@@ -384,7 +384,7 @@ object 3 class array type double rank 0 items     5184 follows
     0.14459E-002   -0.36764E-002   -0.16466E-002
     0.78190E-003   -0.21388E-003   -0.13391E-003
    -0.71292E-004   -0.25972E-004    0.81385E-005
-   -0.75784E-005    0.84210E-004   -0.57027E-004
+   -0.75783E-005    0.84210E-004   -0.57027E-004
     0.24646E-003   -0.15344E-004    0.44974E-003
     0.29483E-002   -0.13186E-002    0.30172E-002
     0.14066E-002   -0.51937E-003    0.13804E-003
@@ -425,7 +425,7 @@ object 3 class array type double rank 0 items     5184 follows
     0.15873E-002   -0.26341E-002    0.28432E-002
     0.49007E-003    0.10263E-001   -0.44098E-001
     0.25985E-003   -0.50604E-002    0.20816E-002
-   -0.97801E-005   -0.13212E-003   -0.22909E-003
+   -0.97796E-005   -0.13212E-003   -0.22909E-003
     0.48134E-003    0.52250E-002   -0.61139E-002
     0.74868E-002   -0.97022E-002    0.12736E-001
    -0.13924E-001    0.13569E-001   -0.16048E-001
@@ -442,13 +442,13 @@ object 3 class array type double rank 0 items     5184 follows
    -0.17468E-001    0.24222E-001   -0.13107E+000
    -0.65242E-001    0.19459E-001   -0.38769E-002
    -0.13998E-002    0.28896E-002   -0.44039E-002
-    0.52052E-002    0.11744E-002    0.25963E-003
+    0.52052E-002    0.11744E-002    0.25964E-003
    -0.21866E-002    0.47172E-002   -0.81182E-002
     0.10154E-001   -0.15684E-001    0.18417E-001
    -0.10597E+000    0.22097E-001    0.78443E-003
    -0.56097E-002    0.55039E-002   -0.44612E-002
     0.32653E-002   -0.22953E-002   -0.13331E-002
-    0.91243E-003   -0.94485E-004   -0.12826E-002
+    0.91243E-003   -0.94484E-004   -0.12826E-002
     0.43961E-002   -0.78443E-002    0.13464E-001
    -0.13779E-002    0.40528E-001   -0.22036E-002
     0.10425E-001   -0.96531E-003   -0.13430E-002
@@ -512,13 +512,13 @@ object 3 class array type double rank 0 items     5184 follows
     0.11827E-001   -0.45014E-002    0.27467E-002
    -0.41543E-003   -0.71183E-003    0.52608E-003
    -0.64382E-003    0.45191E-003    0.50605E-003
-   -0.44980E-003    0.37809E-003   -0.38388E-004
+   -0.44981E-003    0.37809E-003   -0.38389E-004
    -0.49061E-003   -0.81143E-003    0.86459E-002
    -0.45388E-002   -0.19539E-001   -0.35704E-002
-   -0.21204E-002    0.67039E-003    0.70119E-003
+   -0.21204E-002    0.67038E-003    0.70119E-003
    -0.74427E-003    0.55233E-003   -0.45289E-003
    -0.11702E-002    0.10513E-002   -0.10446E-002
-    0.48184E-003   -0.52832E-003    0.40688E-002
+    0.48184E-003   -0.52833E-003    0.40688E-002
    -0.13663E-001   -0.53287E-002    0.80893E-001
     0.13554E-001    0.87640E-003   -0.12860E-002
    -0.94409E-003    0.13653E-002   -0.14728E-002
@@ -570,12 +570,12 @@ object 3 class array type double rank 0 items     5184 follows
     0.55487E-003    0.57562E-002   -0.85141E-003
     0.10230E-001    0.16214E-002   -0.31963E-002
     0.16965E-002   -0.39151E-003    0.11883E-003
-    0.27054E-005   -0.64436E-004    0.29371E-004
+    0.27053E-005   -0.64436E-004    0.29371E-004
    -0.24818E-003    0.15603E-003   -0.36597E-003
    -0.15165E-003   -0.30508E-003   -0.55843E-002
     0.25615E-002   -0.87369E-002   -0.12896E-002
     0.21029E-002   -0.12728E-002    0.23925E-003
-   -0.20980E-003   -0.40398E-004   -0.37869E-004
+   -0.20980E-003   -0.40397E-004   -0.37869E-004
    -0.22762E-004    0.97304E-004   -0.13256E-003
     0.76121E-004    0.46124E-003   -0.11364E-003
     0.51685E-002   -0.25639E-002    0.77172E-002
@@ -627,7 +627,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.13873E-001    0.13771E-001   -0.15353E-001
     0.19554E-001   -0.31206E-001    0.64687E-002
     0.12878E+000    0.43115E+000    0.18311E+000
-   -0.42341E-001    0.49587E-002    0.50176E-002
+   -0.42341E-001    0.49588E-002    0.50176E-002
    -0.10381E-001    0.12020E-001   -0.13237E-001
    -0.18428E-001    0.21596E-001   -0.25230E-001
     0.33125E-001   -0.42929E-001    0.59353E-001
@@ -693,12 +693,12 @@ object 3 class array type double rank 0 items     5184 follows
    -0.13202E-001   -0.15081E-001    0.28654E-002
     0.45947E-002   -0.39497E-002    0.16991E-002
    -0.85009E-003    0.46037E-003   -0.41389E-003
-   -0.11503E-004   -0.26360E-004    0.13328E-004
+   -0.11503E-004   -0.26361E-004    0.13328E-004
     0.44265E-003   -0.10259E-002   -0.89230E-003
     0.43360E-002    0.12999E-001    0.67878E-002
    -0.14383E-001   -0.53637E-003    0.27114E-002
    -0.14313E-002    0.43554E-003   -0.55232E-004
-    0.54550E-004   -0.19917E-002    0.19778E-002
+    0.54549E-004   -0.19917E-002    0.19778E-002
    -0.22171E-002    0.17858E-002   -0.28501E-002
     0.81796E-002   -0.15748E-001   -0.97599E-002
     0.11465E-001    0.41396E-001   -0.12368E-001
@@ -737,7 +737,7 @@ object 3 class array type double rank 0 items     5184 follows
     0.33287E-001   -0.21712E-001    0.12598E-001
    -0.78119E-002    0.22442E-002   -0.20161E-001
     0.21504E-001   -0.24273E-001    0.27271E-001
-   -0.28503E-001    0.16461E-001   -0.41419E-004
+   -0.28503E-001    0.16461E-001   -0.41414E-004
    -0.12990E+000    0.75360E-001   -0.11560E+000
    -0.19544E-001    0.27969E-001   -0.25346E-001
     0.21675E-001   -0.20092E-001    0.19462E-001
@@ -766,7 +766,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.47737E-003   -0.51835E-004    0.58766E-003
    -0.52596E-003    0.72315E-003   -0.11079E-001
    -0.25431E-001   -0.12595E-001    0.68054E-002
-   -0.18857E-002    0.60829E-004    0.13868E-003
+   -0.18857E-002    0.60830E-004    0.13868E-003
    -0.55933E-003    0.34562E-003   -0.15041E-003
     0.80074E-004   -0.32555E-003    0.67842E-003
    -0.15202E-002    0.14050E-002   -0.80795E-003
@@ -798,7 +798,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.27721E-002    0.29741E-002   -0.49061E-003
    -0.72566E-002    0.14443E-001   -0.11927E-001
     0.82051E-001    0.95570E-002    0.10700E-002
-   -0.33922E-004    0.14627E-003    0.88681E-003
+   -0.33919E-004    0.14627E-003    0.88681E-003
    -0.13081E-002    0.21604E-002    0.33550E-002
    -0.40840E-002    0.36977E-002   -0.35055E-002
     0.41269E-003    0.67781E-002    0.27814E-002
@@ -892,9 +892,9 @@ object 3 class array type double rank 0 items     5184 follows
     0.63672E-002   -0.57904E-002    0.46308E-002
    -0.36396E-002   -0.26400E-002    0.17391E-002
    -0.14131E-002    0.78246E-003   -0.61051E-003
-    0.63366E-003    0.24693E-001    0.29656E-001
+    0.63365E-003    0.24693E-001    0.29656E-001
     0.13438E+000    0.27901E-001   -0.22954E-001
-    0.12869E-001   -0.76758E-002    0.58582E-002
+    0.12869E-001   -0.76757E-002    0.58582E-002
    -0.46806E-002    0.36183E-002    0.68827E-002
    -0.57133E-002    0.56860E-002   -0.66211E-002
     0.99125E-002   -0.15797E-001   -0.52503E-002
@@ -908,7 +908,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.45900E-001    0.36916E-001   -0.30142E-001
     0.26465E-001    0.50030E-001   -0.48827E-001
     0.51561E-001   -0.58944E-001    0.74179E-001
-   -0.94716E-001    0.36687E-001   -0.46168E+000
+   -0.94715E-001    0.36687E-001   -0.46168E+000
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@@ -1216,7 +1216,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1234,8 +1234,8 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1273,7 +1273,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1298,7 +1298,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1310,7 +1310,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1330,7 +1330,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1383,7 +1383,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1395,7 +1395,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1523,13 +1523,13 @@ object 3 class array type double rank 0 items     5184 follows
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     0.39700E-002   -0.84627E-004   -0.65947E-003
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@@ -1555,7 +1555,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1602,7 +1602,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -1726,7 +1726,7 @@ object 3 class array type double rank 0 items     5184 follows
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    -0.23530E-004   -0.27346E-003    0.79396E-003
diff --git AmberTools/test/nab/huv.O.4.dx.check AmberTools/test/nab/huv.O.4.dx.check
index add5688..c409ca4 100644
--- AmberTools/test/nab/huv.O.4.dx.check
+++ AmberTools/test/nab/huv.O.4.dx.check
@@ -42,10 +42,10 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -55,10 +55,10 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -74,7 +74,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -172,7 +172,7 @@ object 3 class array type double rank 0 items     5184 follows
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@@ -181,7 +181,7 @@ object 3 class array type double rank 0 items     5184 follows
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     0.12391E-003   -0.17626E-003    0.37440E-002
    -0.73418E-002   -0.43798E-001    0.49519E-002
     0.14953E-002    0.20774E-002   -0.22890E-002
-    0.11235E-002    0.53678E-004    0.34160E-004
+    0.11235E-002    0.53679E-004    0.34160E-004
    -0.92654E-003    0.75587E-003   -0.15990E-002
     0.13713E-002   -0.14112E-002    0.18715E-002
    -0.44715E-002    0.85039E-002    0.41635E-001
@@ -1534,13 +1534,13 @@ object 3 class array type double rank 0 items     5184 follows
     0.11901E-002   -0.16300E-002    0.17072E-002
    -0.20384E-002    0.41606E-002   -0.83538E-002
    -0.36935E-001   -0.18397E-003    0.75164E-003
-    0.32749E-004   -0.54313E-004   -0.55384E-003
+    0.32749E-004   -0.54314E-004   -0.55384E-003
     0.59897E-003   -0.55366E-003   -0.85402E-003
     0.60344E-003   -0.12434E-002    0.99286E-003
    -0.13524E-002    0.82954E-003   -0.21224E-002
     0.41911E-002    0.38989E-001   -0.21565E-002
     0.91862E-003   -0.97115E-003    0.27219E-003
-    0.52312E-005   -0.71291E-003    0.34833E-003
+    0.52313E-005   -0.71291E-003    0.34833E-003
    -0.48047E-003    0.23123E-003   -0.44657E-003
     0.33067E-003   -0.41250E-003    0.10632E-003
    -0.22842E-002    0.73852E-002    0.61030E-002
@@ -1574,7 +1574,7 @@ object 3 class array type double rank 0 items     5184 follows
     0.99674E-002   -0.24989E-002    0.30342E-003
    -0.53277E-003    0.79955E-003   -0.21966E-003
    -0.59661E-003    0.35264E-003   -0.65872E-004
-    0.11436E-002    0.38480E-003   -0.35781E-002
+    0.11436E-002    0.38479E-003   -0.35781E-002
     0.36223E-002   -0.75229E-002    0.15451E-001
     0.40636E-002   -0.14021E-001    0.68264E-002
    -0.25865E-002    0.28621E-002   -0.14937E-002
@@ -1607,7 +1607,7 @@ object 3 class array type double rank 0 items     5184 follows
    -0.72048E-002    0.52170E-002   -0.32634E-002
    -0.19081E-002    0.22332E-002   -0.24117E-002
     0.23217E-002    0.50866E-003   -0.17204E-002
-   -0.75871E-002    0.73309E-002    0.25632E-005
+   -0.75871E-002    0.73309E-002    0.25651E-005
    -0.21416E-001   -0.12367E-001    0.49953E-002
    -0.41626E-002    0.41883E-002   -0.30311E-002
     0.19037E-002    0.31388E-003   -0.26396E-003
@@ -1640,8 +1640,8 @@ object 3 class array type double rank 0 items     5184 follows
     0.33179E-003   -0.34087E-003    0.23211E-003
    -0.32071E-003   -0.56331E-004    0.14792E-003
    -0.41476E-003   -0.10262E-002   -0.21101E-001
-   -0.94099E-004   -0.10972E-002    0.73413E-003
-   -0.43772E-003   -0.10434E-003    0.72385E-004
+   -0.94100E-004   -0.10972E-002    0.73413E-003
+   -0.43772E-003   -0.10434E-003    0.72384E-004
    -0.27691E-003   -0.27499E-003    0.40064E-003
    -0.26074E-003    0.46773E-003   -0.13622E-003
     0.20913E-003   -0.18338E-003    0.73660E-003
@@ -1683,7 +1683,7 @@ object 3 class array type double rank 0 items     5184 follows
     0.38887E-003   -0.10225E-003   -0.35480E-003
     0.21989E-002   -0.46306E-002    0.27804E-001
    -0.46260E-001    0.99268E-001   -0.12849E-001
-    0.69339E-002   -0.28353E-002    0.32796E-002
+    0.69340E-002   -0.28353E-002    0.32796E-002
    -0.19358E-002    0.10950E-002   -0.18272E-003
     0.56051E-002   -0.38298E-002    0.13655E-003
     0.13715E-002   -0.54991E-002    0.85791E-002
diff --git AmberTools/test/nab/rismion.nab AmberTools/test/nab/rismion.nab
new file mode 100644
index 0000000..bcb1bc3
--- /dev/null
+++ AmberTools/test/nab/rismion.nab
@@ -0,0 +1,22 @@
+molecule m;
+float 	m_xyz[dynamic], f_xyz[dynamic], v_xyz[dynamic];
+float 	dgrad, fret;
+int 	ier, i; 
+
+m = getpdb("Na+.pdb");
+readparm(m, "Na+.parm7");
+allocate m_xyz[3*m.natoms];
+allocate f_xyz[3*m.natoms];
+allocate v_xyz[3*m.natoms];
+mm_options( "e_debug=0, ntpr=1, ntpr_md=1, cut=999.0, dt=0.001, rattle=0, tempi=0, zerov=0");
+mm_options( "rism=1, apply_rism_force=0");
+mm_options( "buffer=12, solvcut=999");
+mm_options( "progress=1, xvvfile=../rism1d/spc/spc-nacl.xvv.save");
+mme_init( m, NULL, "::Z", m_xyz, NULL);
+
+setxyz_from_mol( m, NULL, m_xyz );
+
+ier = md(3*m.natoms,0,m_xyz,f_xyz,v_xyz, mme );
+
+if(mytaskid==0)
+  printf( "md returns %d\n", ier );
diff --git AmberTools/test/nab/rismion.out.check AmberTools/test/nab/rismion.out.check
new file mode 100644
index 0000000..38f642a
--- /dev/null
+++ AmberTools/test/nab/rismion.out.check
@@ -0,0 +1,24 @@
+Reading parm file (Na+.parm7)
+title:
+                                                                                
+	mm_options:  e_debug=0
+	mm_options:  ntpr=1
+	mm_options:  ntpr_md=1
+	mm_options:  cut=999.0
+	mm_options:  dt=0.001
+	mm_options:  rattle=0
+	mm_options:  tempi=0
+	mm_options:  zerov=0
+	mm_options:  rism=1
+	mm_options:  apply_rism_force=0
+	mm_options:  buffer=12
+	mm_options:  solvcut=999
+	mm_options:  progress=1
+	mm_options:  xvvfile=../rism1d/spc/spc-nacl.xvv.save
+| New format PARM file being parsed.
+| Version =    0.001 Date = 04:06:10 Time = 16:41:39
+      iter    Total       bad      vdW     elect   nonpolar   genBorn      frms
+  nblist_box, number of atoms= 1
+  nblist_box, number of pairs= 0
+ff:     0    -73.97      0.00      0.00      0.00      0.00    -73.97  0.00e+00
+md returns 0
-----------------------------------------------------------------------------
Workarounds: none

********> bugfix 6
Author: Dave Case (reported by Kevin Wiehe)
Date:   2010/06/29

Programs: NAB

Description: When gbsa=1 and mme2() is called, some experimental code
             for nonpolar contributions is included, which is both 
             undocumented an incorrect.  This patch also prevents users
             from using values for gbsa other that 0 or 1.

To apply the patch:
cd $AMBERHOME
patch -p0 -N < bugfix.6

---------------------------------------------------------------------------
--- AmberTools/src/sff/sff2.c
+++ AmberTools/src/sff/sff2.c
@@ -4557,7 +4557,7 @@ REAL_T egb2(INT_T * lpears, INT_T * upears, INT_T ** pearlist,
             qi2h = 0.5 * qi * qi;
             qid2h = qi2h * dielfac;
 
-            if ((gbsa == 1) || (gbsa == 4) || (gbsa == 5)) {
+            if ((gbsa == 4) || (gbsa == 5)) {
                vdwdenom = 1.0 / (ri + rwater);
                vdwterm =
                    alphanp * (prm->Gvdw[i]) * vdwdenom * vdwdenom *

--- AmberTools/src/sff/mm_options.l
+++ AmberTools/src/sff/mm_options.l
@@ -75,7 +75,7 @@ use_lower_tri[=\ ][01]  	{ ECHO; use_lower_tri = atoi( &yytext[14] ); }
 dynamic_loops[=\ ][01]  	{ ECHO; dynamic_loops = atoi( &yytext[14] ); }
 static_arrays[=\ ][01]  	{ ECHO; static_arrays = atoi( &yytext[14] ); }
 blocksize[=\ ][0-9]+		{ ECHO; blocksize = atoi( &yytext[10] ); }
-gbsa[=\ ][0-5]	                { ECHO; gbsa = atoi( &yytext[5] ); }
+gbsa[=\ ][01]	                { ECHO; gbsa = atoi( &yytext[5] ); }
 dim[=\ ][34]                    { ECHO; dim = atoi( &yytext[4] ); }
 
 rism[=\ ][01]                   { ECHO; rismData.rism = atoi( &yytext[5] ); }
-----------------------------------------------------------------------------
Workarounds: none

********> bugfix 7
Author: Mengjuei Hsieh and Ray Luo
Date:   2010/07/23

Programs: PBSA

Description: Due to the new default value of cutres since Amber11/AT1.4,
             it's possible a number of maximal numbers in PBSA to encounter
             integer overflow. This fix protects most of the variables in
             the setup stage.

To apply the patch:
cd $AMBERHOME
patch -p0 -N < bugfix.7

---------------------------------------------------------------------------
--- AmberTools/src/pbsa/pb_init.f
+++ AmberTools/src/pbsa/pb_init.f
@@ -153,6 +153,7 @@ subroutine pb_init(ifcap,natom,nres,ntypes,nbonh,nbona,ipres,iac,ico,numex,natex
      
    integer ires, iatm, jatm, maxmax, ic, i, j, jp, idum
    integer alloc_err(64)
+   _REAL_ maxnbr_l, maxnba_l
    _REAL_ rinchk
    _REAL_ ucrgh(natom), ucrga(natom)
    character (len=4) :: residue, resid(natom)
@@ -207,16 +208,24 @@ subroutine pb_init(ifcap,natom,nres,ntypes,nbonh,nbona,ipres,iac,ico,numex,natex
     
    ! allocate pb nblists
     
-   maxnba = natom * ( sqrt( max(cutnb,cutsa,cutfd) ) )**3 / 3.0d0
-   maxnbr = natom * ( sqrt( cutres ) + 3.0d0 )**3 / 3.0d0
+   maxnba_l = dble(natom) * ( sqrt( max(cutnb,cutsa,cutfd) ) )**3 / 3.0d0
+   maxnbr_l = dble(natom) * ( sqrt( cutres ) + 3.0d0 )**3 / 3.0d0
    if ( natom >= 65536 ) then
       write(6,'(a)') "PB Warnning: natom**2 exceeds integer limit (2147483647)."
       maxmax = 2147483647
    else
       maxmax = ceiling(dble(natom)/2*dble(natom))
-   endif
-   if ( maxnba > maxmax ) maxnba = maxmax
-   if ( maxnbr > maxmax ) maxnbr = maxmax
+   end if
+   if ( maxnbr_l > maxmax ) then
+      maxnbr = maxmax
+   else
+      maxnbr = int(maxnbr_l)
+   end if
+   if ( maxnba_l > maxmax ) then
+      maxnba = maxmax
+   else
+      maxnba = int(maxnba_l)
+   end if
 
    allocate( iar1pb (6,0:natom), stat = alloc_err(24) )
    allocate( iprshrt(  maxnba ), stat = alloc_err(25) )
-----------------------------------------------------------------------------
Workarounds: none

********> bugfix 8
Author: Andreas W Goetz
Date:   2010/08/04

Programs: SQM

Description: Fix DFTB in SQM which did not work.
             DFTB has been tested for geometry optimization of NMA. 
             It yields the same result as sander (E = -1220.8413).
             This bugfix also includes new tests for DFTB in SQM.

To apply the patch:
cd $AMBERHOME
patch -p0 -N < bugfix.8

---------------------------------------------------------------------------
diff --git AmberTools/src/sqm/sqm.f AmberTools/src/sqm/sqm.f
index 390c73c..ad91121 100644
--- AmberTools/src/sqm/sqm.f
+++ AmberTools/src/sqm/sqm.f
@@ -13,7 +13,7 @@ program sqm
 
    implicit none
 
-   _REAL_ x(3000), f(3000), escf, reff(1000), onereff(1000), work(18000), scf_mchg(1000)
+   _REAL_ x(3000), f(3000), escf, reff(1000), onereff(1000), work(18000)
    character(len=8) atnam(1000)
    _REAL_ born_radii(1000), one_born_radii(1000)
    _REAL_ intdiel, extdiel, Arad
@@ -104,20 +104,23 @@ program sqm
    call allocate_qmgb(qmmm_struct%nquant_nlink)
 
    allocate( qmmm_struct%dxyzqm(3, qmmm_struct%nquant_nlink), stat = ier )
-   REQUIRE(ier == 0) !Deallocated in deallocate qmmm
+   REQUIRE(ier == 0)
+
+   allocate ( qm2_struct%scf_mchg(qmmm_struct%nquant_nlink), stat = ier )
+   REQUIRE(ier == 0)
 
    if (maxcyc < 1) then
       ! ------------------------
       ! Single point calculation
       ! ------------------------
       call sqm_energy(natom, x, escf, born_radii, one_born_radii, &
-                 intdiel, extdiel, Arad, scf_mchg )
+                 intdiel, extdiel, Arad, qm2_struct%scf_mchg )
    else
       ! ---------------------
       ! Geometry optimization
       ! ---------------------
       call xmin(natom, x, f, escf, xmin_iter, maxcyc, born_radii, &
-           one_born_radii, intdiel, extdiel, Arad, scf_mchg, grms_tol, ntpr)
+           one_born_radii, intdiel, extdiel, Arad, qm2_struct%scf_mchg, grms_tol, ntpr)
    end if
 
    ! ----------------
@@ -140,7 +143,7 @@ program sqm
 
    write(6,*) ''
    call qm2_print_charges(1,qmmm_nml%dftb_chg,qmmm_struct%nquant_nlink, &
-                            scf_mchg,qmmm_struct%iqm_atomic_numbers)
+                            qm2_struct%scf_mchg,qmmm_struct%iqm_atomic_numbers)
 
    write(6,*) ''
    write(6,*) 'Final Structure'
@@ -150,6 +153,12 @@ program sqm
    write(6,*) '          --------- Calculation Completed ----------'
    write(6,*)
 
+   deallocate( qmmm_struct%dxyzqm, stat = ier )
+   REQUIRE(ier == 0)
+
+   deallocate ( qm2_struct%scf_mchg, stat = ier )
+   REQUIRE(ier == 0)
+
    call mexit(6,0)
 
 end program sqm
diff --git AmberTools/test/check_slko_files.x AmberTools/test/check_slko_files.x
new file mode 100755
index 0000000..a24edba
--- /dev/null
+++ AmberTools/test/check_slko_files.x
@@ -0,0 +1,14 @@
+#!/bin/csh -f
+#checks if cc.spl file exists - if it does then it
+#assumes that all slko files are installed.
+
+if( -r $AMBERHOME/dat/slko/C-C.skf ) then
+    #Exists
+    exit(0)
+else
+   echo "DFTB SLKO files not found - Skipping DFTB tests..."
+   echo ""
+   exit(1)
+endif
+
+
diff --git AmberTools/test/sqm/nma/Run AmberTools/test/sqm/nma/Run
index 190a0ec..5d3019f 100755
--- AmberTools/test/sqm/nma/Run
+++ AmberTools/test/sqm/nma/Run
@@ -3,8 +3,19 @@
 set SQM = ../../../exe/sqm
 set SPDIFF = ../../dacdif
 set GODIFF = "../../dacdif -a 0.01"
-set SPTESTS = (nma.pm3.sp nma.pm6.sp)
-set GOTESTS = (nma.pm3.go nma.pm6.go)
+
+# check if slko files for DFTB are installed
+../../check_slko_files.x
+if( $status > 0) then
+  # no slko files - do not run DFTB tests
+  set SPTESTS = (nma.pm3.sp nma.pm6.sp)
+  set GOTESTS = (nma.pm3.go nma.pm6.go)
+else
+  # slko files present - run DFTB tests
+  set SPTESTS = (nma.pm3.sp nma.pm6.sp nma.dftb.sp)
+  set GOTESTS = (nma.pm3.go nma.pm6.go nma.dftb.go)
+endif
+
 
 # single point tests
 foreach i ($SPTESTS)
diff --git AmberTools/test/sqm/nma/nma.dftb.go.in AmberTools/test/sqm/nma/nma.dftb.go.in
new file mode 100644
index 0000000..4baa902
--- /dev/null
+++ AmberTools/test/sqm/nma/nma.dftb.go.in
@@ -0,0 +1,30 @@
+Run DFTB geometry optimization for NMA
+ &qmmm
+    qm_theory    = 'DFTB',
+    qmcharge     = 0,
+    ! SCF settings
+    scfconv      = 1.0d-10, ! kcal/mol
+    errconv      = 1.d-06,  ! au
+    tight_p_conv = 0,
+    diag_routine = 1,
+    itrmax       = 100,
+    ! Geometry optimization settings
+    maxcyc       = 100,
+    grms_tol     = 0.001,   ! kcal/(mol*A)
+    ! Output
+    ntpr         = 101,
+    verbosity    = 0,
+ /
+ 6 C    -0.767000     3.380000     4.245000
+ 6 C    -1.809707     2.570219     4.710852
+ 7 N    -2.661673     2.646098     3.869189
+ 6 C    -3.662846     1.855199     3.619926
+ 8 O    -1.634379     2.116691     5.584678
+ 1 H     0.218271     3.164467     4.684075
+ 1 H    -0.578839     3.210298     3.174581
+ 1 H    -1.024346     4.421330     4.488732
+ 1 H    -2.569216     3.204198     3.074324
+ 1 H    -3.347225     0.824359     3.812610
+ 1 H    -4.529359     1.998602     4.311686
+ 1 H    -4.036138     1.906340     2.552627
+
diff --git AmberTools/test/sqm/nma/nma.dftb.go.out.save AmberTools/test/sqm/nma/nma.dftb.go.out.save
new file mode 100644
index 0000000..2fa9f32
--- /dev/null
+++ AmberTools/test/sqm/nma/nma.dftb.go.out.save
@@ -0,0 +1,81 @@
+            --------------------------------------------------------
+                             AMBER SQM VERSION 1.4
+ 
+                                     By
+              Ross C. Walker, Michael F. Crowley, Scott Brozell,
+                Tim Giese, Andreas W. Goetz and David A. Case
+ 
+            --------------------------------------------------------
+ 
+
+--------------------------------------------------------------------------------
+  QM CALCULATION INFO
+--------------------------------------------------------------------------------
+
+| QMMM: Citation for AMBER QMMM Run:
+| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
+
+| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run:
+| QMMM:   Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 5655, (2007)
+
+
+QMMM: SINGLET STATE CALCULATION
+QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 15
+
+| QMMM: *** SCF convergence criteria ***
+| QMMM: Energy change                :  0.1D-09 kcal/mol
+| QMMM: Error matrix |FP-PF|         :  0.1D-05 au
+| QMMM: Density matrix change        :  0.5D-06
+| QMMM: Maximum number of SCF cycles :      100
+ DFTB: Number of atom types =    4
+
+ Parameter files:
+     TYP (AT)  TYP (AT)     SK integral FILE
+|  1  1  (C )   1  (C )     /Users/andi/sources/amber/dat/slko/C-C.skf
+|  2  1  (C )   2  (N )     /Users/andi/sources/amber/dat/slko/C-N.skf
+|  3  1  (C )   3  (O )     /Users/andi/sources/amber/dat/slko/C-O.skf
+|  4  1  (C )   4  (H )     /Users/andi/sources/amber/dat/slko/C-H.skf
+|  5  2  (N )   1  (C )     /Users/andi/sources/amber/dat/slko/N-C.skf
+|  6  2  (N )   2  (N )     /Users/andi/sources/amber/dat/slko/N-N.skf
+|  7  2  (N )   3  (O )     /Users/andi/sources/amber/dat/slko/N-O.skf
+|  8  2  (N )   4  (H )     /Users/andi/sources/amber/dat/slko/N-H.skf
+|  9  3  (O )   1  (C )     /Users/andi/sources/amber/dat/slko/O-C.skf
+| 10  3  (O )   2  (N )     /Users/andi/sources/amber/dat/slko/O-N.skf
+| 11  3  (O )   3  (O )     /Users/andi/sources/amber/dat/slko/O-O.skf
+| 12  3  (O )   4  (H )     /Users/andi/sources/amber/dat/slko/O-H.skf
+| 13  4  (H )   1  (C )     /Users/andi/sources/amber/dat/slko/H-C.skf
+| 14  4  (H )   2  (N )     /Users/andi/sources/amber/dat/slko/H-N.skf
+| 15  4  (H )   3  (O )     /Users/andi/sources/amber/dat/slko/H-O.skf
+| 16  4  (H )   4  (H )     /Users/andi/sources/amber/dat/slko/H-H.skf
+
+--------------------------------------------------------------------------------
+  RESULTS
+--------------------------------------------------------------------------------
+
+  ... geometry converged !
+
+ Heat of formation   =      -1220.84132946 kcal/mol  (      -52.93965264 eV)
+ Total SCF energy    =      -8463.39103876 kcal/mol  (     -367.00017513 eV)
+ 
+    Atomic Charges for Step       1 :
+  Atom    Element       Mulliken Charge
+     1      C                 -0.279
+     2      C                  0.493
+     3      N                 -0.250
+     4      C                 -0.073
+     5      O                 -0.507
+     6      H                  0.096
+     7      H                  0.073
+     8      H                  0.073
+     9      H                  0.186
+    10      H                  0.097
+    11      H                  0.045
+    12      H                  0.045
+ Total Mulliken Charge =       0.000
+ 
+ 
+ Final Structure
+
+
+           --------- Calculation Completed ----------
+
diff --git AmberTools/test/sqm/nma/nma.dftb.sp.in AmberTools/test/sqm/nma/nma.dftb.sp.in
new file mode 100644
index 0000000..45ac9e0
--- /dev/null
+++ AmberTools/test/sqm/nma/nma.dftb.sp.in
@@ -0,0 +1,30 @@
+Run PM3 single point calculation for NMA
+ &qmmm
+    qm_theory    = 'DFTB',
+    qmcharge     = 0,
+    ! SCF settings
+    scfconv      = 1.0d-10, ! kcal/mol
+    errconv      = 1.d-06,  ! au
+    tight_p_conv = 0,
+    diag_routine = 1,
+    itrmax       = 100,
+    ! Geometry optimization settings
+    maxcyc       = 0,
+    grms_tol     = 0.02,   ! kcal/(mol*A)
+    ! Output
+    ntpr         = 10,
+    verbosity    = 0,
+ /
+ 6 C    -0.767000     3.380000     4.245000
+ 6 C    -1.809707     2.570219     4.710852
+ 7 N    -2.661673     2.646098     3.869189
+ 6 C    -3.662846     1.855199     3.619926
+ 8 O    -1.634379     2.116691     5.584678
+ 1 H     0.218271     3.164467     4.684075
+ 1 H    -0.578839     3.210298     3.174581
+ 1 H    -1.024346     4.421330     4.488732
+ 1 H    -2.569216     3.204198     3.074324
+ 1 H    -3.347225     0.824359     3.812610
+ 1 H    -4.529359     1.998602     4.311686
+ 1 H    -4.036138     1.906340     2.552627
+
diff --git AmberTools/test/sqm/nma/nma.dftb.sp.out.save AmberTools/test/sqm/nma/nma.dftb.sp.out.save
new file mode 100644
index 0000000..1cf51f2
--- /dev/null
+++ AmberTools/test/sqm/nma/nma.dftb.sp.out.save
@@ -0,0 +1,111 @@
+            --------------------------------------------------------
+                             AMBER SQM VERSION 1.4
+ 
+                                     By
+              Ross C. Walker, Michael F. Crowley, Scott Brozell,
+                Tim Giese, Andreas W. Goetz and David A. Case
+ 
+            --------------------------------------------------------
+ 
+
+--------------------------------------------------------------------------------
+  QM CALCULATION INFO
+--------------------------------------------------------------------------------
+
+| QMMM: Citation for AMBER QMMM Run:
+| QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008
+
+| QMMM: DFTB Calculation - Additional citation for AMBER DFTB QMMM Run:
+| QMMM:   Seabra, G.M., Walker, R.C. et al., J. PHYS. CHEM. A., 111, 5655, (2007)
+
+
+QMMM: SINGLET STATE CALCULATION
+QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 15
+
+| QMMM: *** SCF convergence criteria ***
+| QMMM: Energy change                :  0.1D-09 kcal/mol
+| QMMM: Error matrix |FP-PF|         :  0.1D-05 au
+| QMMM: Density matrix change        :  0.5D-06
+| QMMM: Maximum number of SCF cycles :      100
+ DFTB: Number of atom types =    4
+
+ Parameter files:
+     TYP (AT)  TYP (AT)     SK integral FILE
+|  1  1  (C )   1  (C )     /Users/andi/sources/amber/dat/slko/C-C.skf
+|  2  1  (C )   2  (N )     /Users/andi/sources/amber/dat/slko/C-N.skf
+|  3  1  (C )   3  (O )     /Users/andi/sources/amber/dat/slko/C-O.skf
+|  4  1  (C )   4  (H )     /Users/andi/sources/amber/dat/slko/C-H.skf
+|  5  2  (N )   1  (C )     /Users/andi/sources/amber/dat/slko/N-C.skf
+|  6  2  (N )   2  (N )     /Users/andi/sources/amber/dat/slko/N-N.skf
+|  7  2  (N )   3  (O )     /Users/andi/sources/amber/dat/slko/N-O.skf
+|  8  2  (N )   4  (H )     /Users/andi/sources/amber/dat/slko/N-H.skf
+|  9  3  (O )   1  (C )     /Users/andi/sources/amber/dat/slko/O-C.skf
+| 10  3  (O )   2  (N )     /Users/andi/sources/amber/dat/slko/O-N.skf
+| 11  3  (O )   3  (O )     /Users/andi/sources/amber/dat/slko/O-O.skf
+| 12  3  (O )   4  (H )     /Users/andi/sources/amber/dat/slko/O-H.skf
+| 13  4  (H )   1  (C )     /Users/andi/sources/amber/dat/slko/H-C.skf
+| 14  4  (H )   2  (N )     /Users/andi/sources/amber/dat/slko/H-N.skf
+| 15  4  (H )   3  (O )     /Users/andi/sources/amber/dat/slko/H-O.skf
+| 16  4  (H )   4  (H )     /Users/andi/sources/amber/dat/slko/H-H.skf
+
+  QMMM: QM Region Cartesian Coordinates (*=link atom) 
+  QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
+  QMMM:     1        1      C       -0.7670    3.3800    4.2450
+  QMMM:     2        2      C       -1.8097    2.5702    4.7109
+  QMMM:     3        3      N       -2.6617    2.6461    3.8692
+  QMMM:     4        4      C       -3.6628    1.8552    3.6199
+  QMMM:     5        5      O       -1.6344    2.1167    5.5847
+  QMMM:     6        6      H        0.2183    3.1645    4.6841
+  QMMM:     7        7      H       -0.5788    3.2103    3.1746
+  QMMM:     8        8      H       -1.0243    4.4213    4.4887
+  QMMM:     9        9      H       -2.5692    3.2042    3.0743
+  QMMM:    10       10      H       -3.3472    0.8244    3.8126
+  QMMM:    11       11      H       -4.5294    1.9986    4.3117
+  QMMM:    12       12      H       -4.0361    1.9063    2.5526
+
+--------------------------------------------------------------------------------
+  RESULTS
+--------------------------------------------------------------------------------
+
+
+ Heat of formation   =      -1039.27301701 kcal/mol  (      -45.06625979 eV)
+ Total SCF energy    =      -8281.82272631 kcal/mol  (     -359.12678229 eV)
+ Electronic energy   =      -8895.69306749 kcal/mol  (     -385.74619780 eV)
+ Core-core repulsion =        613.87034117 kcal/mol  (       26.61941551 eV)
+ 
+    Atomic Charges for Step       1 :
+  Atom    Element       Mulliken Charge
+     1      C                 -0.347
+     2      C                  0.560
+     3      N                 -0.202
+     4      C                 -0.066
+     5      O                 -0.439
+     6      H                  0.077
+     7      H                  0.048
+     8      H                  0.072
+     9      H                  0.187
+    10      H                  0.044
+    11      H                  0.029
+    12      H                  0.037
+ Total Mulliken Charge =       0.000
+ 
+ 
+ Final Structure
+
+  QMMM: QM Region Cartesian Coordinates (*=link atom) 
+  QMMM: QM_NO.   MM_NO.  ATOM         X         Y         Z
+  QMMM:     1        1      C       -0.7670    3.3800    4.2450
+  QMMM:     2        2      C       -1.8097    2.5702    4.7109
+  QMMM:     3        3      N       -2.6617    2.6461    3.8692
+  QMMM:     4        4      C       -3.6628    1.8552    3.6199
+  QMMM:     5        5      O       -1.6344    2.1167    5.5847
+  QMMM:     6        6      H        0.2183    3.1645    4.6841
+  QMMM:     7        7      H       -0.5788    3.2103    3.1746
+  QMMM:     8        8      H       -1.0243    4.4213    4.4887
+  QMMM:     9        9      H       -2.5692    3.2042    3.0743
+  QMMM:    10       10      H       -3.3472    0.8244    3.8126
+  QMMM:    11       11      H       -4.5294    1.9986    4.3117
+  QMMM:    12       12      H       -4.0361    1.9063    2.5526
+
+           --------- Calculation Completed ----------
+
---------------------------------------------------------------------------
Workarounds: none

********> bugfix 9
cd $AMBERHOME
patch -p0 -N < bugfix 9 

Author: Daniel R. Roe
Date: 2010-07-16
Programs: ptraj
Description: Fixes reading of hex values on big endian machines which 
             prevented correct identification of files and/or reading 
             incorrect number of frames in gzipped trajectory files. 
             Use unsigned char instead of uint8_t for compatibility 
             with obsolete compilers. Also fix calculation of # frames 
             in Amber Trajectories by switching to long long int (to be 
             consistent with the stat struct) and clean up the bitwise 
             arithmetic in gzipFileSize().
             Fixes two bugs in clustering code: 1) If no atoms are selected
             in RMS mask resulting NULL mask, segfault would occur and 
             2) Pointer was being compared like an integer; the check would 
             result in no initialization and a segfault.

-----------------------------------------------------------------------------
--- AmberTools/src/ptraj/ptraj.c	2010-07-16 20:27:16.000000000 -0400
+++ AmberTools/src/ptraj/ptraj.c	2010-07-16 20:56:55.000000000 -0400
@@ -2058,7 +2058,8 @@
   int lines_per_set;
   int start = 1;
   int stop = 1;
-  int frame_lines, frame_size, title_size, seekable, file_size;
+  int frame_lines, title_size, seekable;
+  long long int file_size, frame_size;
   long int endoffset;
   float *binposScratch;
   FILE *fp;
@@ -2417,20 +2418,29 @@
 
       // Determine Uncompressed File Size for Nframes calculation
       file_size=0;
-      if (trajInfo->compressType==1) // Gzip
+      if (trajInfo->compressType==1)      // Gzip
         file_size=gzipFileSize(filename);
       else if (trajInfo->compressType==2) // Bzip2
         file_size=bzip2FileSize(filename);
       else if (trajInfo->compressType==3) // Zip
         file_size=zipFileSize(filename);
-      if (file_size<0) return NULL;
+      if (file_size<0) {
+        fprintf(stdout,
+                "ERROR in %s: Could not calculate uncompressed file size for %s\n",
+                ROUTINE, filename);
+        return NULL;
+      }
       if (file_size==0) file_size=frame_stat.st_size;
 
       if (prnlev>0)
-        fprintf(stdout,"[%i] Title offset %u   Frame Size %u    File size %lu\n",
+        fprintf(stdout,"[%i] Title offset %u   Frame Size %u    File size %lli\n",
                 worldrank,trajInfo->titleSize,trajInfo->frameSize,file_size);
-      trajInfo->Nframes = (int) ((file_size - trajInfo->titleSize) / trajInfo->frameSize);
-      if (((file_size - trajInfo->titleSize) % (trajInfo->frameSize)) == 0) {
+      frame_size = (long long int) trajInfo->titleSize;
+      file_size = file_size - frame_size; // Subtract title size from file total size.
+      frame_size = (long long int) trajInfo->frameSize;
+      trajInfo->Nframes = (int) (file_size / frame_size);
+      if (prnlev>0) fprintf(stdout,"    File has %i frames.\n",trajInfo->Nframes);
+      if ( (file_size % frame_size) == 0 ) {
 	seekable = 1;
 	stop = trajInfo->Nframes;
       } else {
--- AmberTools/src/ptraj/io.c	2010-07-01 00:41:40.000000000 -0400
+++ AmberTools/src/ptraj/io.c	2010-07-16 21:51:04.000000000 -0400
@@ -673,14 +673,15 @@
   }
 }
 
-/* DAN ROE:
- * gzipFileSize()
- * Return the uncompressed size in bytes of gzipped file by peeking at the 
- * last 4 bytes.
+/* gzipFileSize()
+ * DRR: Return the uncompressed size in bytes of gzipped file by peeking 
+ * at the last 4 bytes.
+ * NOTE: long long int should be equivalent to off_t. 
  */
-int gzipFileSize(char *filename) {
+long long int gzipFileSize(char *filename) {
   FILE *infile;
-  int b1,b2,b3,b4,val;
+  unsigned char b1,b2,b3,b4;
+  long long int val,temp;
 
   if (filename==NULL) return -1;
   if ( (infile = fopen(filename,"rb"))==NULL ) {
@@ -697,21 +698,35 @@
   fread(&b2,1,1,infile);
   fread(&b1,1,1,infile);
 
-  val = (b1 << 24) | (b2 << 16) + (b3 << 8) + b4;
+  val = 0;
+  temp = (long long int) b1;
+  temp <<= 24;
+  val = val | temp;
+  temp = (long long int) b2;
+  temp <<= 16;
+  val = val | temp;
+  temp = (long long int) b3;
+  temp <<= 8;
+  val = val | temp;
+  temp = (long long int) b4;
+  val = val | temp;
+
+  //val = (b1 << 24) | (b2 << 16) + (b3 << 8) + b4;
 
   fclose(infile);
 
-  if (prnlev>0) fprintf(stdout,"gzipFileSize: Uncompressed size of %s: %i\n",filename,val);
+  if (prnlev>0) fprintf(stdout,"gzipFileSize: Uncompressed size of %s: %lli\n",filename,val);
 
   return val;
 }
-/* DAN ROE: 
+
+/* 
  * bzip2FileSize()
- * Return the uncompressed size of bzip2 file in bytes by counting all 
- * characters using bzcat and wc.
+ * DRR: Return the uncompressed size of bzip2 file in bytes by counting 
+ * all characters using bzcat and wc.
  */
-int bzip2FileSize(char *filename) {
-  int val;
+long long int bzip2FileSize(char *filename) {
+  long long int val;
   char *command;
   FILE *pipe;
 
@@ -724,20 +739,21 @@
     fprintf(stdout,"       Check that bzcat and wc are present on your system.\n");
     return -1;
   }
-  fscanf(pipe,"%i",&val);
+  fscanf(pipe,"%lli",&val);
   pclose(pipe);
 
-  if (prnlev>0) fprintf(stdout,"bzip2FileSize: Uncompressed size of %s: %i\n",filename,val);
+  if (prnlev>0) fprintf(stdout,"bzip2FileSize: Uncompressed size of %s: %lli\n",filename,val);
 
   return val;
 }
-/* DAN ROE: 
+
+/* 
  * zipFileSize()
- * Return the uncompressed size of zip file in bytes by counting all 
- * characters using unzip and wc.
+ * DRR: Return the uncompressed size of zip file in bytes by counting 
+ * all characters using unzip and wc.
  */
-int zipFileSize(char *filename) {
-  int val;
+long long int zipFileSize(char *filename) {
+  long long int val;
   char *command;
   FILE *pipe;
 
@@ -750,10 +766,10 @@
     fprintf(stdout,"       Check that unzip and wc are present on your system.\n");
     return -1;
   }
-  fscanf(pipe,"%i",&val);
+  fscanf(pipe,"%lli",&val);
   pclose(pipe);
 
-  if (prnlev>0) fprintf(stdout,"zipFileSize: Uncompressed size of %s: %i\n",filename,val);
+  if (prnlev>0) fprintf(stdout,"zipFileSize: Uncompressed size of %s: %lli\n",filename,val);
 
   return val;
 }
@@ -774,7 +790,7 @@
  *  -2: Internal error
  */
 int id_Filesig(char *filename, FILE *infile) {
-  int *h;
+  unsigned char *h;
   int i, type;
 
   /* Check that either filename or infile is specified, but not both */
@@ -797,7 +813,7 @@
     rewind(infile);
 
   /* Read first 3 bytes from file */
-  h=(int*) calloc(3,sizeof(int));
+  h=(unsigned char*) calloc(3,sizeof(unsigned char));
   fread(h,1,1,infile);
   fread(h+1,1,1,infile);
   fread(h+2,1,1,infile);
--- AmberTools/src/ptraj/io.h	2010-07-16 20:26:17.000000000 -0400
+++ AmberTools/src/ptraj/io.h	2010-07-16 20:26:56.000000000 -0400
@@ -76,9 +76,9 @@
 
 extern void doSystem(char *);
 extern char * promptToOpenFile( FILE **, char *, char *, char *);
-extern int gzipFileSize(char *);
-extern int bzip2FileSize(char *);
-extern int zipFileSize(char *);
+extern long long int gzipFileSize(char *);
+extern long long int bzip2FileSize(char *);
+extern long long int zipFileSize(char *);
 extern int id_Filesig(char *,FILE *);
 extern int openFile( FILE **, char *, char *);
 extern int  promptUserResponse(FILE *, FILE *, char *, char *, int);
@@ -97,9 +97,9 @@
 
 extern void doSystem();
 extern char * promptToOpenFile();
-extern int gzipFileSize();
-extern int bzip2FileSize();
-extern int zipFileSize();
+extern long long int gzipFileSize();
+extern long long int bzip2FileSize();
+extern long long int zipFileSize();
 extern int id_Filesig();
 extern int openFile();
 extern int  promptUserResponse();
--- AmberTools/src/ptraj/actions.c	2010-07-26 09:30:41.462276836 -0400
+++ AmberTools/src/ptraj/actions.c	2010-07-26 09:31:36.767408649 -0400
@@ -3655,6 +3655,8 @@
         {
             action->mask = processAtomMask("*", action->state);
         }
+        if (action->mask==NULL) 
+          return INVALID_ARGUMENTS_RETURN_CODE;
         /* Create a new "substate" trajInfo->state containing only some atoms: */
         modifyStateByMask(&trajInfo->state, &action->state, action->mask, 0);
         trajInfo->atoms = trajInfo->state->atoms;
--- AmberTools/src/ptraj/cluster.c	2010-07-26 22:48:49.998157908 -0400
+++ AmberTools/src/ptraj/cluster.c	2010-07-26 22:51:04.023535647 -0400
@@ -4041,7 +4041,7 @@
 		OutputTrajInfo = (trajectoryInfo*)action->carg2;
     }
 
-    if (!FirstOutputFlag)
+    if (FirstOutputFlag==NULL)
     {
       FirstOutputFlag = (int*)SafeMalloc(__FILE__, __LINE__, sizeof(int) * This->ClusterCount);
       memset(FirstOutputFlag, 1, sizeof(int) * This->ClusterCount);
---------------------------------------------------------------------------
Workarounds: none

********> bugfix 10
cd $AMBERHOME
patch -p0 -N < bugfix.10

Author: Jason Swails
Date: 2010-08-31
Programs: nab
Description: If a dihedral parameter had a periodicity of 6, it would not be recognized, but without
             a "break;" statement it would push on to default: case on some (if not all) systems,
             causing the program to exit even though it was a valid choice, with the error message:
             bad periodicity: 6

-----------------------------------------------------------------------------
diff --git AmberTools/src/sff/sff2.c AmberTools/src/sff/sff2.c
index 3a196b8..f45d1d3 100644
--- AmberTools/src/sff/sff2.c
+++ AmberTools/src/sff/sff2.c
@@ -1384,6 +1384,7 @@ REAL_T ephi2(int nphi, int *a1, int *a2,
          e = ct2 * (ct2 * (ct2 * 32.0 - 48.0) + 18.0) - 1.0;
          df = ct * (ct2 * (ct2 * 192.0 - 192.0) + 36.0);
          ddf = ct2 * (ct2 * 960.0 - 576.0) + 36.0;
+         break;
 
       default:
          fprintf(stderr, "bad periodicity: %d\n", iper);
---------------------------------------------------------------------------
Workarounds: none

********> bugfix 11
cd $AMBERHOME
patch -p0 -N < bugfix.11

Author: Andreas W Goetz
Date: 2010-09-13
Programs: sqm
Description: fix d orbitals for DFTB 
             DFTB code did not work with d orbitals
             Fixed by not checking for parameter value MAX_VALENCE_ORBITALS
             which is not used by the DFTB code

-----------------------------------------------------------------------------
diff --git AmberTools/src/sqm/qm2_load_params_and_allocate.f AmberTools/src/sqm/qm2_load_params_and_allocate.f
index 57b43d4..2b6fa63 100644
--- AmberTools/src/sqm/qm2_load_params_and_allocate.f
+++ AmberTools/src/sqm/qm2_load_params_and_allocate.f
@@ -136,9 +136,12 @@ subroutine qm2_load_params_and_allocate()
          n_atomic_orb=natomic_orbs(iqm_atomic)
          if (n_atomic_orb>1) nheavy_atoms=nheavy_atoms+1
          ! Check we don't bust any static arrays
-         if (n_atomic_orb > MAX_VALENCE_ORBITALS) then
-            write (6,*) 'n_atomic_orb of ',n_atomic_orb,' exceeds max_valence_orbitals of MAX_VALENCE_ORBITALS'
-            call sander_bomb('qm2_load_params.f','exceeded max','Check qmmm_module.f and parameters.h')
+         ! DFTB is independent of this and checks are done in qm2_dftb_load_params
+         if ( .not. qmmm_nml%qmtheory%DFTB ) then
+            if (n_atomic_orb > MAX_VALENCE_ORBITALS) then
+               write (6,*) 'n_atomic_orb of ',n_atomic_orb,' exceeds max_valence_orbitals of MAX_VALENCE_ORBITALS'
+               call sander_bomb('qm2_load_params.f','exceeded max','Check qmmm_module.f and parameters.h')
+            end if
          end if
          qm2_params%natomic_orbs(i)=n_atomic_orb
          qm2_params%orb_loc(1,i)=qm2_struct%norbs+1
diff --git AmberTools/src/sqm/qmmm_module.f AmberTools/src/sqm/qmmm_module.f
index 6bafddd..1745226 100644
--- AmberTools/src/sqm/qmmm_module.f
+++ AmberTools/src/sqm/qmmm_module.f
@@ -84,7 +84,7 @@ module qmmm_module
   !--------- SIZE / ARRAY LIMITATIONS -----------------------
   
         ! Locks maximum valence orbitals at 4 = S,P (no D or F - code is not present)
-  integer, parameter :: MAX_VALENCE_ORBITALS =4 
+  integer, parameter :: MAX_VALENCE_ORBITALS = 4
   integer, parameter :: MAX_VALENCE_DIMENSION = MAX_VALENCE_ORBITALS*(MAX_VALENCE_ORBITALS+1)/2
   
   !----------------------------------------------------------
---------------------------------------------------------------------------
Workarounds: none

********> bugfix 12 
cd $AMBERHOME
patch -p0 -N < bugfix.12

Author: Daniel R. Roe
Date: 2010-09-10
Programs: ptraj
Description: Fixes issue where ptraj would segfault when reading an input
             file that had no EOL.  

-----------------------------------------------------------------------------
--- AmberTools/src/ptraj/ptraj.c	2010-09-10 09:16:54.442548223 -0400
+++ AmberTools/src/ptraj/ptraj.c	2010-09-10 09:20:16.175692377 -0400
@@ -7165,8 +7165,8 @@
      */
 
   argumentStack = NULL;
-  while ( (bufferp = fgets(buffer, BUFFER_SIZE, infile)) != NULL &&
-	  strcmp(bufferp, "go\n") != 0 ) {
+  while ( (bufferp = fgets(buffer, BUFFER_SIZE, infile)) != NULL ) {
+    if ( strncmp(bufferp, "go", 2) == 0 ) break;
 
     continuation = bufferp;
     while ( continuation != NULL ) {
---------------------------------------------------------------------------
Workarounds: none

********> bugfix 13 

Author: Wei Zhang
Date: 2010-09-24
Programs: sleap
Description: Fixes issues that arise when proteins with disulfide bonds
             are used with the amoeba force fiels
             Apply this patch from the $AMBEHROME directory

-----------------------------------------------------------------------------
--- AmberTools/src/gleap/plugins/loadpdb.cpp
+++ AmberTools/src/gleap/plugins/loadpdb.cpp
@@ -31,28 +31,29 @@ namespace amber
             throw std::runtime_error( "Error: file " + m_file + " doesn't exist" );
         }
 
-
         molecule_ptr pmol( new molecule_t() );
 
         read_pdb( is, *pmol );
 
         string disulf = "auto";
 	mortenv().get_s("disulfide", disulf);
-        console_t* pcon = (disulf=="auto") ? NULL : console().get();
+        if( disulf!="off" )
+        {
+            console_t* pcon = (disulf=="auto") ? NULL : console().get();
 
-	double disulfcut = 2.1;
-	string tmp;
-	if( mortenv().get_s("disulfcut", tmp) )
-	{
-	    disulfcut = atof( tmp.c_str() );
-	}
+            double disulfcut = 2.1;
+            string tmp;
+            if( mortenv().get_s("disulfcut", tmp) )
+            {
+	        disulfcut = atof( tmp.c_str() );
+            }
 
-        disulfide( *pmol, disulfcut, pcon );
+            disulfide( *pmol, disulfcut, pcon );
+        }
 
         namemap_ptr nmap = content().get_nmap( "_namemap" );
         if( nmap != NULL )
         {
- 
             if( m_action=="loadpdb" )
             {
                 mdlize_mdb( *pmol, content() );
diff --git a/dat/leap/lib/amoeba_amino.off b/dat/leap/lib/amoeba_amino.off
index 87180a5..677d804 100644
--- dat/leap/lib/amoeba_amino.off
+++ dat/leap/lib/amoeba_amino.off
@@ -880,23 +880,23 @@
 !entry.CYX.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt dbl chg str
  "N" "7" 0 1 131072 1 7 -0.435921 
  "H" "10" 0 1 131072 2 1 0.290077 
- "CA" "8" 0 1 131072 3 6 -0.030547 
+ "CA" "44" 0 1 131072 3 6 -0.030547 
  "HA" "12" 0 1 131072 4 1 0.132146 
- "CB" "" 0 1 131072 5 6 -0.033006 
- "HB2" "" 0 1 131072 6 1 0.078951 
- "HB3" "" 0 1 131072 7 1 0.078951 
- "SG" "" 0 1 131072 8 16 -0.132272 
+ "CB" "45" 0 1 131072 5 6 -0.033006 
+ "HB2" "46" 0 1 131072 6 1 0.078951 
+ "HB3" "46" 0 1 131072 7 1 0.078951 
+ "SG" "49" 0 1 131072 8 16 -0.132272 
  "C" "9" 0 1 131072 9 6 0.624788 
  "O" "11" 0 1 131072 10 8 -0.573167 
 !entry.CYX.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
  "N" "7" 0 -1 0.0
  "H" "10" 0 -1 0.0
- "CA" "8" 0 -1 0.0
+ "CA" "44" 0 -1 0.0
  "HA" "12" 0 -1 0.0
- "CB" "" 0 -1 0.0
- "HB2" "" 0 -1 0.0
- "HB3" "" 0 -1 0.0
- "SG" "" 0 -1 0.0
+ "CB" "45" 0 -1 0.0
+ "HB2" "46" 0 -1 0.0
+ "HB3" "46" 0 -1 0.0
+ "SG" "49" 0 -1 0.0
  "C" "9" 0 -1 0.0
  "O" "11" 0 -1 0.0
 !entry.CYX.unit.boundbox array dbl
@@ -990,16 +990,16 @@
  "H" "10" 0 -1 0.0
  "CA" "8" 0 -1 0.0
  "HA" "12" 0 -1 0.0
- "CB" "" 0 -1 0.0
- "HB2" "" 0 -1 0.0
- "HB3" "" 0 -1 0.0
- "CG" "" 0 -1 0.0
- "HG2" "" 0 -1 0.0
- "HG3" "" 0 -1 0.0
- "CD" "" 0 -1 0.0
- "OE1" "" 0 -1 0.0
- "OE2" "" 0 -1 0.0
- "HE2" "" 0 -1 0.0
+ "CB" "144" 0 -1 0.0
+ "HB2" "145" 0 -1 0.0
+ "HB3" "145" 0 -1 0.0
+ "CG" "146" 0 -1 0.0
+ "HG2" "147" 0 -1 0.0
+ "HG3" "147" 0 -1 0.0
+ "CD" "148" 0 -1 0.0
+ "OE1" "149" 0 -1 0.0
+ "OE2" "149" 0 -1 0.0
+ "HE2" "10" 0 -1 0.0
  "C" "9" 0 -1 0.0
  "O" "11" 0 -1 0.0
 !entry.GLH.unit.boundbox array dbl
@@ -2147,21 +2147,21 @@
  "H" "10" 0 -1 0.0
  "CA" "8" 0 -1 0.0
  "HA" "12" 0 -1 0.0
- "CB" "" 0 -1 0.0
- "HB2" "" 0 -1 0.0
- "HB3" "" 0 -1 0.0
- "CG" "" 0 -1 0.0
- "HG2" "" 0 -1 0.0
- "HG3" "" 0 -1 0.0
- "CD" "" 0 -1 0.0
- "HD2" "" 0 -1 0.0
- "HD3" "" 0 -1 0.0
- "CE" "" 0 -1 0.0
- "HE2" "" 0 -1 0.0
- "HE3" "" 0 -1 0.0
- "NZ" "" 0 -1 0.0
- "HZ2" "" 0 -1 0.0
- "HZ3" "" 0 -1 0.0
+ "CB" "159" 0 -1 0.0
+ "HB2" "160" 0 -1 0.0
+ "HB3" "160" 0 -1 0.0
+ "CG" "161" 0 -1 0.0
+ "HG2" "162" 0 -1 0.0
+ "HG3" "162" 0 -1 0.0
+ "CD" "163" 0 -1 0.0
+ "HD2" "164" 0 -1 0.0
+ "HD3" "164" 0 -1 0.0
+ "CE" "165" 0 -1 0.0
+ "HE2" "166" 0 -1 0.0
+ "HE3" "166" 0 -1 0.0
+ "NZ" "167" 0 -1 0.0
+ "HZ2" "168" 0 -1 0.0
+ "HZ3" "168" 0 -1 0.0
  "C" "9" 0 -1 0.0
  "O" "11" 0 -1 0.0
 !entry.LYN.unit.boundbox array dbl
diff --git a/dat/leap/lib/amoeba_aminoct.off b/dat/leap/lib/amoeba_aminoct.off
index 23e47b7..a43878f 100644
--- dat/leap/lib/amoeba_aminoct.off
+++ dat/leap/lib/amoeba_aminoct.off
@@ -638,24 +638,24 @@
 !entry.CCYX.unit.atoms table  str name  str type  int typex  int resx  int flags  int seq  int elmnt dbl chg str
  "N" "7" 0 1 131072 1 7 -0.382100 
  "H" "10" 0 1 131072 2 1 0.268100 
- "CA" "8" 0 1 131072 3 6 -0.131800 
+ "CA" "44" 0 1 131072 3 6 -0.131800 
  "HA" "12" 0 1 131072 4 1 0.093800 
- "CB" "" 0 1 131072 5 6 -0.194300 
- "HB2" "" 0 1 131072 6 1 0.122800 
- "HB3" "" 0 1 131072 7 1 0.122800 
- "SG" "" 0 1 131072 8 16 -0.052900 
+ "CB" "45" 0 1 131072 5 6 -0.194300 
+ "HB2" "46" 0 1 131072 6 1 0.122800 
+ "HB3" "46" 0 1 131072 7 1 0.122800 
+ "SG" "49" 0 1 131072 8 16 -0.052900 
  "C" "192" 0 1 131072 9 6 0.761800 
  "O" "193" 0 1 131072 10 8 -0.804100 
  "OXT" "193" 0 1 131072 11 8 -0.804100 
 !entry.CCYX.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
  "N" "7" 0 -1 0.0
  "H" "10" 0 -1 0.0
- "CA" "8" 0 -1 0.0
+ "CA" "44" 0 -1 0.0
  "HA" "12" 0 -1 0.0
- "CB" "" 0 -1 0.0
- "HB2" "" 0 -1 0.0
- "HB3" "" 0 -1 0.0
- "SG" "" 0 -1 0.0
+ "CB" "45" 0 -1 0.0
+ "HB2" "46" 0 -1 0.0
+ "HB3" "46" 0 -1 0.0
+ "SG" "49" 0 -1 0.0
  "C" "192" 0 -1 0.0
  "O" "193" 0 -1 0.0
  "OXT" "193" 0 -1 0.0
diff --git a/dat/leap/lib/amoeba_aminont.off b/dat/leap/lib/amoeba_aminont.off
index 073970e..0683de7 100644
--- dat/leap/lib/amoeba_aminont.off
+++ dat/leap/lib/amoeba_aminont.off
@@ -736,12 +736,12 @@
  "H1" "191" 0 1 131072 2 1 0.181500 
  "H2" "191" 0 1 131072 3 1 0.181500 
  "H3" "191" 0 1 131072 4 1 0.181500 
- "CA" "8" 0 1 131072 5 6 0.105500 
+ "CA" "44" 0 1 131072 5 6 0.105500 
  "HA" "12" 0 1 131072 6 1 0.092200 
- "CB" "" 0 1 131072 7 6 -0.027700 
- "HB2" "" 0 1 131072 8 1 0.068000 
- "HB3" "" 0 1 131072 9 1 0.068000 
- "SG" "" 0 1 131072 10 16 -0.098400 
+ "CB" "45" 0 1 131072 7 6 -0.027700 
+ "HB2" "46" 0 1 131072 8 1 0.068000 
+ "HB3" "46" 0 1 131072 9 1 0.068000 
+ "SG" "49" 0 1 131072 10 16 -0.098400 
  "C" "9" 0 1 131072 11 6 0.612300 
  "O" "11" 0 1 131072 12 8 -0.571300 
 !entry.NCYX.unit.atomspertinfo table  str pname  str ptype  int ptypex  int pelmnt  dbl pchg
---------------------------------------------------------------------------
Workarounds: none

********> bugfix 14

Author: Andreas W Goetz
Date: 2010/10/20
Programs: sqm
Description: Fix performance issues of sqm.
	     DIIS related work will now only be done if DIIS is switched
	     on for SCF convergence of difficult cases.
	     Calculations will be approximately 30% faster.

To apply the patch:
cd $AMBERHOME
patch -p0 -N < bugfix.14

-----------------------------------------------------------------------------
diff --git AmberTools/src/sqm/qm2_scf.f AmberTools/src/sqm/qm2_scf.f
index 123ff68..801ca23 100644
--- AmberTools/src/sqm/qm2_scf.f
+++ AmberTools/src/sqm/qm2_scf.f
@@ -33,9 +33,9 @@ subroutine qm2_scf(fock_matrix, hmatrix, W, escf, den_matrix, scf_mchg, num_qmmm
                             qm_gb, qmmm_mpi, qmmm_scratch
     use constants, only : EV_TO_KCAL, zero, two
 
-    use qm2_iterator_mod, only : scf_iterator_value
-    use qm2_iterator_mod, only : diis_iterator_value
-    use qm2_iterator_mod, only : remaining_diis_tokens
+    use qm2_iterator_mod, only : scf_iterator_value     ! this is an integer function
+    use qm2_iterator_mod, only : diis_iterator_value    ! this is an integer function
+    use qm2_iterator_mod, only : remaining_diis_tokens  ! this is an integer function
 
 
     implicit none
@@ -75,21 +75,24 @@ subroutine qm2_scf(fock_matrix, hmatrix, W, escf, den_matrix, scf_mchg, num_qmmm
                                   !again. This is used to force the last few SCF steps to be full diagonalisations.
     logical fock_predict_active !Set to true if we are attempting to predict the fock matrix on this QMMM call.
 
-    logical diis_is_off, errmat_is_converged
     character(len=1) :: fock_extrap_flag
-    logical dont_turn_off_diis
 
+    ! DIIS
+    ! While DIIS will accelerate SCF convergence it will do so at a very high cost
+    ! since Fock matrix builds and diagonalizations for semiempirical methods are
+    ! cheaper than the overhead generated by the matrix multiplications required for DIIS
+    ! Thus switch DIIS only on if we have difficulty in converging the SCF
+    ! switch DIIS on after SCF step 100 if user turns on DIIS by setting ndiis_attempts > 0
+    integer, parameter :: switch_on_diis = 100 ! don't set this to values lower than 3!!!
+    ! switch DIIS on as a last resort if SCF did not converge until iteration 800
+    integer, parameter :: switch_on_diis_last_resort = 800
+    logical diis_is_off, errmat_is_converged, errmat_is_on
+    logical dont_turn_off_diis
     _REAL_ :: errval
 
-! scf_iterator_value is a function
-!    integer :: scf_iterator_value
-
 ! current_scf_errval is a function
     _REAL_ :: current_scf_errval
 
-! remaining_diis_tokens is a function
-!    integer :: remaining_diis_tokens
-
 !qm2_Helect is a function
     _REAL_ qm2_HELECT
 
@@ -141,12 +144,13 @@ subroutine qm2_scf(fock_matrix, hmatrix, W, escf, den_matrix, scf_mchg, num_qmmm
 !    i = remaining_diis_tokens( qmmm_nml%ndiis_attempts )
     i = remaining_diis_tokens( 0 )
     dont_turn_off_diis = .FALSE.
+    diis_is_off = qmmm_nml%ndiis_attempts < 1 .OR. qmmm_nml%ndiis_matrices < 2
+    errmat_is_on = qmmm_nml%errconv < 1.0D-02
+    errval = -1.0D0 ! initialize errval to unrealistic value
 
     fock_extrap_flag = " "
 
 
-
-
     if (qmmm_nml%verbosity > 2 .and. qmmm_mpi%commqmmm_master) then
       write(6,'("QMMM: ")')
       write(6,'("QMMM: SCF Convergence Information")')
@@ -214,8 +218,18 @@ subroutine qm2_scf(fock_matrix, hmatrix, W, escf, den_matrix, scf_mchg, num_qmmm
       energy_diff = scf_energy - eold
 
       if (qmmm_mpi%commqmmm_master) then
-         CALL pack_diis(SIZE(fock_matrix),fock_matrix,den_matrix)
-         errval = current_scf_errval()
+         ! do this only if we need it, this seriously affects performance
+         if ( .not. errmat_is_on ) then
+            ! check if we shall switch calculation of the error matrix on for diis
+            if ( ( ( .not. diis_is_off ) .and. (scf_iteration+qmmm_nml%ndiis_matrices >= switch_on_diis) ) &
+                 .or. (scf_iteration+qmmm_nml%ndiis_matrices >= switch_on_diis_last_resort) ) then
+               errmat_is_on = .true.
+            end if
+         end if
+         if ( errmat_is_on ) then
+            CALL pack_diis(SIZE(fock_matrix),fock_matrix,den_matrix)
+            errval = current_scf_errval()
+         end if
       end if
 
 
@@ -290,7 +304,7 @@ subroutine qm2_scf(fock_matrix, hmatrix, W, escf, den_matrix, scf_mchg, num_qmmm
            ! IF THE USER REQUESTED US TO!! The default value of 
            ! qmmm_nml%ndiis_attempts is 0, so this requires a form
            ! of human intervention
-           if ( scf_iteration == 100 ) then
+           if ( scf_iteration == switch_on_diis ) then
               i = remaining_diis_tokens( qmmm_nml%ndiis_attempts )
               dont_turn_off_diis = .TRUE.
               
@@ -306,7 +320,7 @@ subroutine qm2_scf(fock_matrix, hmatrix, W, escf, den_matrix, scf_mchg, num_qmmm
            ! turn the (default OFF) diis parameters on.
            ! I guess we should turn diis ON for the user.
            ! I mean, we're at iteration #800.  What else can we do?
-           if ( scf_iteration == 800 ) then
+           if ( scf_iteration == switch_on_diis_last_resort ) then
               i = remaining_diis_tokens( 100 )
               dont_turn_off_diis = .TRUE.
               
@@ -329,8 +343,8 @@ subroutine qm2_scf(fock_matrix, hmatrix, W, escf, den_matrix, scf_mchg, num_qmmm
 !           end if
            
 
-           diis_is_off = qmmm_nml%ndiis_attempts < 1 .OR. qmmm_nml%ndiis_matrices < 2
-           errmat_is_converged = errval < qmmm_nml%errconv !.OR. diis_is_off
+           ! Is the error matrix converged? Set to true if we don't check for the error matrix
+           errmat_is_converged = errval < qmmm_nml%errconv .OR. ( .not. errmat_is_on )
 
            
            if (abs(energy_diff) < qmmm_nml%scfconv .AND. &
@@ -379,7 +393,7 @@ subroutine qm2_scf(fock_matrix, hmatrix, W, escf, den_matrix, scf_mchg, num_qmmm
      ! We have decided that we have not converged
      ! We must diagonalize a fock matrix so that the next iteration can form a new guess
      ! density matrix, provided a set of trial orbitals
-     if (qmmm_mpi%commqmmm_master) then
+     if (qmmm_mpi%commqmmm_master .and. (.not. diis_is_off) .and. ( scf_iteration >= switch_on_diis ) ) then
         CALL diis_extrap( qm2_struct%matsize, fock_matrix , fock_extrap_flag )
      end if
      
@@ -1941,10 +1955,6 @@ SUBROUTINE diis_extrap(npf,pf,extrap_flag)
   _REAL_,intent(out) :: pf(npf) ! packed fock matrix
   character(len=1),intent(out) :: extrap_flag
 
-!  integer :: scf_iterator_value
-!  integer :: diis_iterator_value
-!  integer :: diis_iterator_prev_value
-!  integer :: remaining_diis_tokens
   _REAL_  :: current_scf_errval
 
   logical :: HAVE_DIIS_DATA
@@ -1975,7 +1985,6 @@ SUBROUTINE diis_extrap(npf,pf,extrap_flag)
   ERR_IS_SMALL     = current_scf_errval() < 0.5d0
   HAVE_DIIS_TOKENS = remaining_diis_tokens() > 0
   EXTRAPOLATE      = HAVE_DIIS_DATA .AND. ERR_IS_SMALL .AND. HAVE_DIIS_TOKENS
-
   IF ( .NOT. EXTRAPOLATE ) THEN
      pf = qm2_struct%diis_fock( : , diis_idx )
      RETURN
---------------------------------------------------------------------------
Workarounds: none

********> bugfix.15 
cd $AMBERHOME
patch -p0 -N < bugfix.15

Author: Daniel R. Roe
Date: 2010-10-07
Programs: ptraj
Description: Fixes issue where output of cluster trajectory could cause a 
             segfault when trajectory became too large (filestack was not
             properly cleared).
             Also fix minor issue in secstruct (DSSP) code where atom 
             indices were not being correctly initialized, leading to 
             minor inconsistencies in turn population calculation with
             residues without one or more of the following atoms: H, C,
             N, O.

-----------------------------------------------------------------------------
--- AmberTools/src/ptraj/cluster.c	2010-10-07 17:02:51.928036297 -0400
+++ AmberTools/src/ptraj/cluster.c	2010-10-07 17:03:48.046160351 -0400
@@ -4089,7 +4089,7 @@
 		     *  to avoid crashing out if we hit the OS-level file-size limit: 
 		     */
 		  FileNumber[ClusterIndex] = FileNumber[ClusterIndex] + 1;
-		  fclose(OutputFiles[ClusterIndex]);
+		  safe_fclose(OutputFiles[ClusterIndex]);
 		  FirstOutputFlag[ClusterIndex] = 1;
 		  FirstFlag = 1;      
 	        }
--- AmberTools/src/ptraj/actions.c      2010-09-09 10:29:51.204345479 -0400
+++ AmberTools/src/ptraj/actions.c      2010-10-06 19:00:10.000000000 -0400
@@ -16408,6 +16413,10 @@
       residues[i].antiparallelSheetProb = 0; 
       residues[i].turnProb = 0;
       residues[i].isActive = 0;
+      residues[i].H=-1;
+      residues[i].C=-1;
+      residues[i].N=-1;
+      residues[i].O=-1;
     }
     actRes = 0;
     for (i = 0; i < action->state->atoms; i++) {
---------------------------------------------------------------------------
Workarounds: none

********> bugfix.16 
cd $AMBERHOME
patch -p0 -N < bugfix.16

Author: Daniel R. Roe
Date: 2010-08-11 
Description:
Fix file seeking in ptraj for large (>2GB) files.

-----------------------------------------------------------------------------
--- AmberTools/src/ptraj/trajectory.c	2010-11-05 16:11:44.497971494 -0400
+++ AmberTools/src/ptraj/trajectory.c	2010-11-05 16:14:39.102729060 -0400
@@ -2341,15 +2341,22 @@
 
 /* trajFile_fseek()
  * Wrapper for fseek. Seek to a given frame. 
+ * fseeko is used for better compatibility with large files. To avoid
+ * losing bits each variable is explicitly converted to off_t in offset 
+ * calculation.
  */
 int trajFile_fseek(coordinateInfo *C, int frame) {
   int err;
+  off_t offset;
 
   if (C==NULL) return -1;
 
-  if (C->isMPI==0) 
-    err=fseek(C->file, C->titleSize+(frame*C->frameSize), SEEK_SET);
-  else
+  if (C->isMPI==0) {
+    offset = (off_t) frame;
+    offset *= (off_t) C->frameSize;
+    offset += (off_t) C->titleSize;
+    err=fseeko(C->file, offset, SEEK_SET);
+  } else
     err=parallel_fseek(C,frame);
 
   return err;
-----------------------------------------------------------------------------
Workarounds: none