XPLOR-NIH version 2.18-pre4 C.D. Schwieters, J.J. Kuszewski, Progr. NMR Spectr. 48, 47-62 (2006). N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih based on X-PLOR 3.851 by A.T. Brunger User: schwitrs on: tan (x86_64/Linux ) at: 11-Jun-07 15:29:03 X-PLOR>remarks XPACK.INP X-PLOR>remarks test the crystallographic packing facility X-PLOR> X-PLOR>parameter @TOPPAR:param19.pro end ASSFIL: file /home/schwitrs/xplor/toppar/param19.pro opened. PARRDR>remark - parameter file PARAM19 - PARRDR>remark PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) PARRDR>remark TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) PARRDR>remark JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 PARRDR> PARRDR>set echo=false end PARRDR> end X-PLOR> X-PLOR>{* read a ca trace *} X-PLOR>struc STRUcture>PSF REMARKS FILENAME="TH:[BRUNGER.XREFIN.LACTAL]JUNK.PSF;1" REMARKS - parameter file PARAM19 - REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) REMARKS JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 REMARKS DATE: 8-SEP-86 14:23:44 created by user: BRUNGER XPLOR: current counts (number in parenthesis is maximum) NATOM= 123(MAXA= 200) NBOND= 0(MAXB= 100) NTHETA= 0(MAXT= 100) NGRP= 123(MAXGRP= 200) NPHI= 0(MAXP= 100) NIMPHI= 0(MAXIMP= 100) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 0(MAXNB= 100) STRUcture>end X-PLOR> X-PLOR>coor COOR>REMARK FILENAME="TH:[BRUNGER.XREFIN.LACTAL]JUNK.PDB;1" COOR>REMARK - parameter file PARAM19 - COOR>REMARK PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974) COOR>REMARK TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976) COOR>REMARK JORGENSEN NONBOND PARAMETERS JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1 COOR>REMARK DATE: 8-SEP-86 14:23:36 created by user: BRUNGER COOR>ATOM 1 CA LYS 1 7.781 27.092 15.335 0.00 12.00 COOR>ATOM 2 CA GLN 2 8.641 26.707 11.942 0.00 12.00 X-PLOR> X-PLOR> X-PLOR> X-PLOR>{===================================================================} X-PLOR> X-PLOR>xrefin XREFINE> a=33.6 b=69.9 c=47.3 alpha=90.0 beta=90.0 gamma=90.0 XREFINE> XREFINE> {* space_group=P2(1)2(1)2 *} XREFINE> symmetry=(x,y,z) XREFINE> symmetry=(-x,-y,z) XREFINE> symmetry=(1/2+x,1/2-y,-z) XREFINE> symmetry=(1/2-x,1/2+y,-z) XREFINE>end X-PLOR> X-PLOR>parameter PARRDR> nbonds cutnb=7.0 wmin=0.5 ctonnb=5.0 ctofnb=6.0 end PARRDR>end X-PLOR> X-PLOR>flags exclude * include pvdw pele end X-PLOR> X-PLOR>distance DISTANCE> cutoff=7.0 cuton=0.0 DISTANCE>end DISTAN: nonbonded distances printed atoms " -18 -TYR -CA " and " -43 -GLU -CA "(XSYM# 1) 6.4299 A apart atoms " -18 -TYR -CA " and " -44 -ASN -CA "(XSYM# 1) 6.7671 A apart atoms " -18 -TYR -CA " and " -45 -ASN -CA "(XSYM# 1) 6.9035 A apart atoms " -65 -GLN -CA " and " -67 -PRO -CA "(XSYM# 2) 5.8728 A apart atoms " -65 -GLN -CA " and " -68 -GLN -CA "(XSYM# 2) 6.5588 A apart atoms " -66 -VAL -CA " and " -66 -VAL -CA "(XSYM# 2) 6.2844 A apart atoms " -66 -VAL -CA " and " -67 -PRO -CA "(XSYM# 2) 5.3431 A apart atoms " -67 -PRO -CA " and " -67 -PRO -CA "(XSYM# 2) 6.0164 A apart atoms " -11 -LEU -CA " and " -62 -LYS -CA "(XSYM# 3) 6.7869 A apart atoms " -11 -LEU -CA " and " -63 -SER -CA "(XSYM# 3) 6.7108 A apart atoms " -14 -ASP -CA " and " -76 -SER -CA "(XSYM# 3) 6.8969 A apart atoms " -32 -HIS -CA " and " -116 -GLU -CA "(XSYM# 3) 5.8469 A apart atoms " -32 -HIS -CA " and " -117 -GLN -CA "(XSYM# 3) 5.5654 A apart atoms " -32 -HIS -CA " and " -118 -TRP -CA "(XSYM# 3) 6.9637 A apart atoms " -33 -THR -CA " and " -115 -LEU -CA "(XSYM# 3) 6.5111 A apart atoms " -33 -THR -CA " and " -116 -GLU -CA "(XSYM# 3) 5.5269 A apart atoms " -33 -THR -CA " and " -117 -GLN -CA "(XSYM# 3) 4.1007 A apart atoms " -34 -SER -CA " and " -114 -LYS -CA "(XSYM# 3) 6.0216 A apart atoms " -34 -SER -CA " and " -115 -LEU -CA "(XSYM# 3) 3.2618 A apart atoms " -34 -SER -CA " and " -116 -GLU -CA "(XSYM# 3) 4.3069 A apart atoms " -34 -SER -CA " and " -117 -GLN -CA "(XSYM# 3) 5.4301 A apart atoms " -35 -GLY -CA " and " -114 -LYS -CA "(XSYM# 3) 6.6834 A apart atoms " -35 -GLY -CA " and " -115 -LEU -CA "(XSYM# 3) 5.3421 A apart atoms " -35 -GLY -CA " and " -116 -GLU -CA "(XSYM# 3) 6.3705 A apart atoms " -40 -ALA -CA " and " -115 -LEU -CA "(XSYM# 3) 6.8380 A apart atoms " -62 -LYS -CA " and " -86 -THR -CA "(XSYM# 3) 6.8612 A apart atoms " -63 -SER -CA " and " -84 -ASP -CA "(XSYM# 3) 5.6054 A apart atoms " -63 -SER -CA " and " -85 -ILE -CA "(XSYM# 3) 5.9031 A apart atoms " -63 -SER -CA " and " -86 -THR -CA "(XSYM# 3) 4.3773 A apart atoms " -64 -SER -CA " and " -83 -ASP -CA "(XSYM# 3) 6.1213 A apart atoms " -64 -SER -CA " and " -84 -ASP -CA "(XSYM# 3) 4.8386 A apart atoms " -64 -SER -CA " and " -85 -ILE -CA "(XSYM# 3) 6.1086 A apart atoms " -64 -SER -CA " and " -86 -THR -CA "(XSYM# 3) 6.8352 A apart atoms " -65 -GLN -CA " and " -84 -ASP -CA "(XSYM# 3) 6.5057 A apart atoms " -76 -SER -CA " and " -86 -THR -CA "(XSYM# 3) 6.7312 A apart atoms " -77 -CYS -CA " and " -86 -THR -CA "(XSYM# 3) 5.0857 A apart atoms " -77 -CYS -CA " and " -87 -ASP -CA "(XSYM# 3) 5.9249 A apart atoms " -78 -ASP -CA " and " -86 -THR -CA "(XSYM# 3) 5.5576 A apart atoms " -78 -ASP -CA " and " -87 -ASP -CA "(XSYM# 3) 5.4141 A apart atoms " -78 -ASP -CA " and " -89 -ILE -CA "(XSYM# 3) 6.2910 A apart atoms " -78 -ASP -CA " and " -90 -MET -CA "(XSYM# 3) 5.2779 A apart atoms " -81 -LEU -CA " and " -87 -ASP -CA "(XSYM# 3) 6.2677 A apart atoms " -81 -LEU -CA " and " -90 -MET -CA "(XSYM# 3) 6.1793 A apart atoms " -105 -LEU -CA " and " -117 -GLN -CA "(XSYM# 3) 6.2857 A apart atoms " -105 -LEU -CA " and " -118 -TRP -CA "(XSYM# 3) 6.6117 A apart atoms " -106 -ALA -CA " and " -117 -GLN -CA "(XSYM# 3) 6.2798 A apart atoms " -106 -ALA -CA " and " -118 -TRP -CA "(XSYM# 3) 5.7339 A apart atoms " -106 -ALA -CA " and " -119 -LEU -CA "(XSYM# 3) 5.5545 A apart atoms " -108 -LYS -CA " and " -123 -LEU -CA "(XSYM# 3) 4.9930 A apart atoms " -109 -ALA -CA " and " -123 -LEU -CA "(XSYM# 3) 5.9068 A apart X-PLOR>distance DISTANCE> cutoff=6. cuton=5.8 DISTANCE>end DISTAN: nonbonded distances printed atoms " -65 -GLN -CA " and " -67 -PRO -CA "(XSYM# 2) 5.8728 A apart atoms " -32 -HIS -CA " and " -116 -GLU -CA "(XSYM# 3) 5.8469 A apart atoms " -63 -SER -CA " and " -85 -ILE -CA "(XSYM# 3) 5.9031 A apart atoms " -77 -CYS -CA " and " -87 -ASP -CA "(XSYM# 3) 5.9249 A apart atoms " -109 -ALA -CA " and " -123 -LEU -CA "(XSYM# 3) 5.9068 A apart X-PLOR> X-PLOR>test first sele=( resid 34 ) step=0.0002 tol=0.0 end SELRPN: 1 atoms have been selected out of 123 TESTFD: Parameters: STEP= 0.00020 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 34 X ( 34 SER CA ) -13.794221 -13.794223 0.000001 34 Y ( 34 SER CA ) 3.998552 3.998552 0.000000 34 Z ( 34 SER CA ) -1.572373 -1.572373 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>{* now skew the unit-cell to test derivatives *} X-PLOR>{* ========================================== *} X-PLOR>xrefin XREFINE> alpha=60.0 beta=70.0 gamma=50.0 XREFINE>end X-PLOR> X-PLOR>distance DISTANCE> cutoff=5.0 cuton=0.0 DISTANCE>end DISTAN: nonbonded distances printed atoms " -19 -GLY -CA " and " -98 -ILE -CA "(XSYM# 2) 4.9250 A apart atoms " -19 -GLY -CA " and " -99 -LYS -CA "(XSYM# 2) 2.8462 A apart atoms " -20 -GLY -CA " and " -99 -LYS -CA "(XSYM# 2) 4.9057 A apart atoms " -43 -GLU -CA " and " -95 -ILE -CA "(XSYM# 2) 4.3525 A apart atoms " -46 -GLU -CA " and " -90 -MET -CA "(XSYM# 2) 4.8368 A apart atoms " -46 -GLU -CA " and " -91 -CYS -CA "(XSYM# 2) 4.1091 A apart atoms " -46 -GLU -CA " and " -92 -ALA -CA "(XSYM# 2) 3.6196 A apart atoms " -46 -GLU -CA " and " -95 -ILE -CA "(XSYM# 2) 3.6128 A apart atoms " -47 -SER -CA " and " -55 -ILE -CA "(XSYM# 2) 3.6422 A apart atoms " -47 -SER -CA " and " -91 -CYS -CA "(XSYM# 2) 3.3394 A apart atoms " -50 -TYR -CA " and " -59 -LEU -CA "(XSYM# 2) 3.5205 A apart atoms " -50 -TYR -CA " and " -60 -TRP -CA "(XSYM# 2) 4.5381 A apart atoms " -55 -ILE -CA " and " -57 -ASN -CA "(XSYM# 2) 4.0749 A apart atoms " -56 -SER -CA " and " -56 -SER -CA "(XSYM# 2) 2.8710 A apart atoms " -56 -SER -CA " and " -57 -ASN -CA "(XSYM# 2) 3.2792 A apart atoms " -57 -ASN -CA " and " -60 -TRP -CA "(XSYM# 2) 4.9739 A apart atoms " -58 -LYS -CA " and " -80 -PHE -CA "(XSYM# 2) 3.8977 A apart atoms " -59 -LEU -CA " and " -79 -LYS -CA "(XSYM# 2) 4.9264 A apart atoms " -59 -LEU -CA " and " -80 -PHE -CA "(XSYM# 2) 2.0067 A apart atoms " -59 -LEU -CA " and " -81 -LEU -CA "(XSYM# 2) 4.5894 A apart atoms " -60 -TRP -CA " and " -77 -CYS -CA "(XSYM# 2) 3.0284 A apart atoms " -60 -TRP -CA " and " -80 -PHE -CA "(XSYM# 2) 4.7794 A apart atoms " -61 -CYS -CA " and " -61 -CYS -CA "(XSYM# 2) 3.3120 A apart atoms " -61 -CYS -CA " and " -75 -ILE -CA "(XSYM# 2) 4.3529 A apart atoms " -61 -CYS -CA " and " -77 -CYS -CA "(XSYM# 2) 3.2795 A apart atoms " -61 -CYS -CA " and " -79 -LYS -CA "(XSYM# 2) 4.9678 A apart atoms " -62 -LYS -CA " and " -75 -ILE -CA "(XSYM# 2) 3.8101 A apart atoms " -63 -SER -CA " and " -73 -CYS -CA "(XSYM# 2) 4.1325 A apart atoms " -65 -GLN -CA " and " -87 -ASP -CA "(XSYM# 2) 4.4508 A apart atoms " -65 -GLN -CA " and " -88 -ASP -CA "(XSYM# 2) 3.8657 A apart atoms " -65 -GLN -CA " and " -91 -CYS -CA "(XSYM# 2) 4.7368 A apart atoms " -68 -GLN -CA " and " -84 -ASP -CA "(XSYM# 2) 3.8533 A apart atoms " -69 -SER -CA " and " -79 -LYS -CA "(XSYM# 2) 3.4188 A apart atoms " -69 -SER -CA " and " -80 -PHE -CA "(XSYM# 2) 2.5203 A apart atoms " -69 -SER -CA " and " -81 -LEU -CA "(XSYM# 2) 4.2847 A apart atoms " -70 -ARG -CA " and " -79 -LYS -CA "(XSYM# 2) 3.6969 A apart atoms " -70 -ARG -CA " and " -80 -PHE -CA "(XSYM# 2) 3.8093 A apart atoms " -70 -ARG -CA " and " -81 -LEU -CA "(XSYM# 2) 2.6799 A apart atoms " -71 -ASN -CA " and " -77 -CYS -CA "(XSYM# 2) 2.7923 A apart atoms " -71 -ASN -CA " and " -78 -ASP -CA "(XSYM# 2) 2.2067 A apart atoms " -71 -ASN -CA " and " -79 -LYS -CA "(XSYM# 2) 2.4800 A apart atoms " -71 -ASN -CA " and " -80 -PHE -CA "(XSYM# 2) 4.8915 A apart atoms " -72 -ILE -CA " and " -77 -CYS -CA "(XSYM# 2) 4.3194 A apart atoms " -72 -ILE -CA " and " -78 -ASP -CA "(XSYM# 2) 3.2538 A apart atoms " -73 -CYS -CA " and " -77 -CYS -CA "(XSYM# 2) 3.7773 A apart atoms " -73 -CYS -CA " and " -78 -ASP -CA "(XSYM# 2) 3.9122 A apart atoms " -74 -ASP -CA " and " -76 -SER -CA "(XSYM# 2) 2.8456 A apart atoms " -74 -ASP -CA " and " -77 -CYS -CA "(XSYM# 2) 4.8028 A apart atoms " -74 -ASP -CA " and " -78 -ASP -CA "(XSYM# 2) 4.2114 A apart atoms " -75 -ILE -CA " and " -75 -ILE -CA "(XSYM# 2) 3.3961 A apart atoms " -75 -ILE -CA " and " -76 -SER -CA "(XSYM# 2) 1.0762 A apart atoms " -75 -ILE -CA " and " -77 -CYS -CA "(XSYM# 2) 4.6642 A apart atoms " -76 -SER -CA " and " -76 -SER -CA "(XSYM# 2) 4.2778 A apart atoms " -93 -LYS -CA " and " -97 -ASP -CA "(XSYM# 2) 3.2592 A apart atoms " -93 -LYS -CA " and " -98 -ILE -CA "(XSYM# 2) 4.5100 A apart atoms " -94 -LYS -CA " and " -97 -ASP -CA "(XSYM# 2) 4.6969 A apart atoms " -96 -LEU -CA " and " -96 -LEU -CA "(XSYM# 2) 4.2807 A apart atoms " -96 -LEU -CA " and " -97 -ASP -CA "(XSYM# 2) 3.7243 A apart atoms " -96 -LEU -CA " and " -99 -LYS -CA "(XSYM# 2) 4.2013 A apart atoms " -97 -ASP -CA " and " -97 -ASP -CA "(XSYM# 2) 3.0698 A apart atoms " -97 -ASP -CA " and " -99 -LYS -CA "(XSYM# 2) 4.6363 A apart atoms " -99 -LYS -CA " and " -100 -GLY -CA "(XSYM# 2) 4.4300 A apart atoms " -118 -TRP -CA " and " -121 -GLU -CA "(XSYM# 2) 3.7080 A apart atoms " -118 -TRP -CA " and " -123 -LEU -CA "(XSYM# 2) 4.5460 A apart atoms " -119 -LEU -CA " and " -119 -LEU -CA "(XSYM# 2) 4.4772 A apart atoms " -119 -LEU -CA " and " -120 -CYS -CA "(XSYM# 2) 3.2276 A apart atoms " -119 -LEU -CA " and " -121 -GLU -CA "(XSYM# 2) 1.9693 A apart atoms " -119 -LEU -CA " and " -122 -LYS -CA "(XSYM# 2) 3.1337 A apart atoms " -119 -LEU -CA " and " -123 -LEU -CA "(XSYM# 2) 3.2918 A apart atoms " -120 -CYS -CA " and " -120 -CYS -CA "(XSYM# 2) 3.5290 A apart atoms " -120 -CYS -CA " and " -123 -LEU -CA "(XSYM# 2) 4.7625 A apart atoms " -1 -LYS -CA " and " -76 -SER -CA "(XSYM# 3) 4.5725 A apart atoms " -1 -LYS -CA " and " -87 -ASP -CA "(XSYM# 3) 3.2349 A apart atoms " -1 -LYS -CA " and " -88 -ASP -CA "(XSYM# 3) 4.3669 A apart atoms " -2 -GLN -CA " and " -76 -SER -CA "(XSYM# 3) 4.9887 A apart atoms " -14 -ASP -CA " and " -84 -ASP -CA "(XSYM# 3) 4.7151 A apart atoms " -17 -GLY -CA " and " -115 -LEU -CA "(XSYM# 3) 4.9810 A apart atoms " -18 -TYR -CA " and " -115 -LEU -CA "(XSYM# 3) 3.7413 A apart atoms " -20 -GLY -CA " and " -116 -GLU -CA "(XSYM# 3) 3.8018 A apart atoms " -20 -GLY -CA " and " -117 -GLN -CA "(XSYM# 3) 3.2735 A apart atoms " -31 -PHE -CA " and " -109 -ALA -CA "(XSYM# 3) 4.7202 A apart atoms " -32 -HIS -CA " and " -109 -ALA -CA "(XSYM# 3) 2.9733 A apart atoms " -32 -HIS -CA " and " -112 -THR -CA "(XSYM# 3) 2.9750 A apart atoms " -32 -HIS -CA " and " -113 -GLU -CA "(XSYM# 3) 2.9240 A apart atoms " -33 -THR -CA " and " -113 -GLU -CA "(XSYM# 3) 2.5870 A apart atoms " -34 -SER -CA " and " -113 -GLU -CA "(XSYM# 3) 3.5281 A apart atoms " -35 -GLY -CA " and " -113 -GLU -CA "(XSYM# 3) 4.8303 A apart atoms " -38 -THR -CA " and " -87 -ASP -CA "(XSYM# 3) 3.9419 A apart atoms " -39 -GLN -CA " and " -86 -THR -CA "(XSYM# 3) 3.0856 A apart atoms " -39 -GLN -CA " and " -87 -ASP -CA "(XSYM# 3) 4.6339 A apart atoms " -82 -ASP -CA " and " -86 -THR -CA "(XSYM# 3) 4.9228 A apart atoms " -82 -ASP -CA " and " -87 -ASP -CA "(XSYM# 3) 4.2886 A apart atoms " -83 -ASP -CA " and " -88 -ASP -CA "(XSYM# 3) 4.4963 A apart atoms " -83 -ASP -CA " and " -89 -ILE -CA "(XSYM# 3) 3.0932 A apart atoms " -1 -LYS -CA " and " -62 -LYS -CA "(XSYM# 4) 3.5799 A apart atoms " -1 -LYS -CA " and " -65 -GLN -CA "(XSYM# 4) 4.7413 A apart atoms " -1 -LYS -CA " and " -66 -VAL -CA "(XSYM# 4) 4.7662 A apart atoms " -2 -GLN -CA " and " -62 -LYS -CA "(XSYM# 4) 3.9265 A apart atoms " -3 -PHE -CA " and " -62 -LYS -CA "(XSYM# 4) 4.3189 A apart atoms " -3 -PHE -CA " and " -64 -SER -CA "(XSYM# 4) 4.6337 A apart atoms " -7 -GLU -CA " and " -64 -SER -CA "(XSYM# 4) 4.9556 A apart atoms " -37 -ASP -CA " and " -66 -VAL -CA "(XSYM# 4) 3.1502 A apart atoms " -38 -THR -CA " and " -66 -VAL -CA "(XSYM# 4) 4.4565 A apart atoms " -39 -GLN -CA " and " -66 -VAL -CA "(XSYM# 4) 4.0110 A apart atoms " -40 -ALA -CA " and " -66 -VAL -CA "(XSYM# 4) 4.3486 A apart X-PLOR> X-PLOR>test first sele=( resid 34 or resid 56 or resid 77 or resid 67 or resid 99 SELRPN> or resid 113 ) step=0.001 tol=0.0 end SELRPN: 6 atoms have been selected out of 123 TESTFD: Parameters: STEP= 0.00100 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 34 X ( 34 SER CA ) 1.097569 1.097569 0.000000 34 Y ( 34 SER CA ) -2.043184 -2.043184 0.000000 34 Z ( 34 SER CA ) -4.404606 -4.404615 0.000008 56 X ( 56 SER CA ) -35.982648 -35.982767 0.000119 56 Y ( 56 SER CA ) -59.156553 -59.157113 0.000559 56 Z ( 56 SER CA ) 53.102477 53.102705 0.000229 67 X ( 67 PRO CA ) -0.088706 -0.088706 0.000000 67 Y ( 67 PRO CA ) 0.057785 0.057785 0.000000 67 Z ( 67 PRO CA ) -0.095476 -0.095476 0.000000 77 X ( 77 CYS CA ) 26.333405 26.333413 0.000009 77 Y ( 77 CYS CA ) 109.419067 109.419425 0.000358 77 Z ( 77 CYS CA ) -114.801432 -114.801672 0.000240 99 X ( 99 LYS CA ) -44.389272 -44.389280 0.000008 99 Y ( 99 LYS CA ) -74.663429 -74.663585 0.000155 99 Z ( 99 LYS CA ) 61.830830 61.830829 0.000002 113 X ( 113 GLU CA ) 234.844630 234.844931 0.000301 113 Y ( 113 GLU CA ) -293.007371 -293.007946 0.000574 113 Z ( 113 GLU CA ) -206.001242 -206.001719 0.000477 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR> X-PLOR>{* now we test the interaction criterium *} X-PLOR>{* ===================================== *} X-PLOR>cons interaction=( resid 99 )=( all ) end SELRPN: 1 atoms have been selected out of 123 SELRPN: 123 atoms have been selected out of 123 X-PLOR> X-PLOR>energy end --------------- cycle= 1 -------------------------------------------------- | Etotal =22.082 grad(E)=7.424 E(PVDW)=20.830 E(PELE)=1.252 | ------------------------------------------------------------------------------- X-PLOR>display $pele 1.2518 X-PLOR>display $pvdw 20.8303 X-PLOR> X-PLOR>cons interaction=( resid 99 )=( resid 96 ) end SELRPN: 1 atoms have been selected out of 123 SELRPN: 1 atoms have been selected out of 123 X-PLOR> X-PLOR>distance DISTANCE> cutoff=7.0 cuton=0.0 DISTANCE>end DISTAN: nonbonded distances printed atoms " -96 -LEU -CA " and " -99 -LYS -CA "(XSYM# 2) 4.2013 A apart X-PLOR> X-PLOR> X-PLOR> X-PLOR>test first sele=( resid 99 or resid 96 ) step=0.001 tol=0.0 end SELRPN: 2 atoms have been selected out of 123 TESTFD: Parameters: STEP= 0.00100 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 96 X ( 96 LEU CA ) 0.440318 0.440318 0.000000 96 Y ( 96 LEU CA ) 0.021821 0.021821 0.000000 96 Z ( 96 LEU CA ) -0.294188 -0.294188 0.000000 99 X ( 99 LYS CA ) 0.440318 0.440318 0.000000 99 Y ( 99 LYS CA ) 0.021821 0.021821 0.000000 99 Z ( 99 LYS CA ) -0.072208 -0.072208 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR> X-PLOR>{* test the automatic update business *} X-PLOR>{* ================================== *} X-PLOR>energy end --------------- cycle= 2 -------------------------------------------------- | Etotal =0.209 grad(E)=0.036 E(PVDW)=0.004 E(PELE)=0.205 | ------------------------------------------------------------------------------- X-PLOR>coor translate sele=( resid 99 ) vector=( 0.0 0.4 0.0 ) end SELRPN: 1 atoms have been selected out of 123 COOR: using atom subset. COOR: translation vector =( 0.000000 0.400000 0.000000 ) COOR: selected coordinates translated X-PLOR>energy end --------------- cycle= 3 -------------------------------------------------- | Etotal =0.208 grad(E)=0.036 E(PVDW)=0.003 E(PELE)=0.205 | ------------------------------------------------------------------------------- X-PLOR>coor translate sele=( resid 99 ) vector=( 0.0 0.2 0.0 ) end SELRPN: 1 atoms have been selected out of 123 COOR: using atom subset. COOR: translation vector =( 0.000000 0.200000 0.000000 ) COOR: selected coordinates translated X-PLOR>energy end --------------- cycle= 4 -------------------------------------------------- | Etotal =0.200 grad(E)=0.034 E(PVDW)=-0.001 E(PELE)=0.201 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>flags incl vdw elec pvdw pele end X-PLOR>cons inter=( resn t* ) ( prev ) end SELRPN: 14 atoms have been selected out of 123 SELRPN: 14 atoms have been selected out of 123 X-PLOR>distance end DISTAN: nonbonded distances printed MAKINB: mode 5 found 0 exclusions, 0 interactions(1-4) and 0 GB exclusions atoms " -29 -THR -CA " and " -33 -THR -CA " 5.1910 A apart atoms " -36 -TYR -CA " and " -38 -THR -CA " 6.3421 A apart atoms " -48 -THR -CA " and " -50 -TYR -CA " 6.4083 A apart atoms " -103 -TYR -CA " and " -104 -TRP -CA " 3.9053 A apart atoms " -48 -THR -CA " and " -60 -TRP -CA "(XSYM# 2) 6.5202 A apart atoms " -50 -TYR -CA " and " -60 -TRP -CA "(XSYM# 2) 4.5381 A apart atoms " -118 -TRP -CA " and " -118 -TRP -CA "(XSYM# 2) 5.7237 A apart atoms " -29 -THR -CA " and " -112 -THR -CA "(XSYM# 3) 6.8194 A apart atoms " -33 -THR -CA " and " -112 -THR -CA "(XSYM# 3) 5.2529 A apart atoms " -38 -THR -CA " and " -86 -THR -CA "(XSYM# 3) 6.1195 A apart X-PLOR> X-PLOR>stop HEAP: maximum use= 636630 current use= 605825 X-PLOR: total CPU time= 0.0600 s X-PLOR: entry time at 15:29:03 11-Jun-07 X-PLOR: exit time at 15:29:03 11-Jun-07