XPLOR-NIH version 2.16.5 C.D. Schwieters, J.J. Kuszewski, based on X-PLOR 3.851 by A.T. Brunger N. Tjandra, and G.M. Clore J. Magn. Res., 160, 66-74 (2003). http://nmr.cit.nih.gov/xplor-nih User: schwitrs on: beige (x86_64/Linux ) at: 22-Feb-07 16:37:38 X-PLOR>remarks dgtest4.inp X-PLOR>remarks test the dg energy term X-PLOR>remarks tests on an ALA polypeptide chain X-PLOR>remarks Axel T. Brunger X-PLOR>remarks ============== X-PLOR> X-PLOR>!--------------- X-PLOR>! test one: random four-atom metrization X-PLOR>!--------------- X-PLOR> X-PLOR> X-PLOR>structure reset end XPLOR: current counts (number in parenthesis is maximum) NATOM= 0(MAXA= 200) NBOND= 0(MAXB= 0) NTHETA= 0(MAXT= 0) NGRP= 0(MAXGRP= 0) NPHI= 0(MAXP= 0) NIMPHI= 0(MAXIMP= 0) NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0) NNB= 0(MAXNB= 0) X-PLOR>topology reset @TOPPAR:topallhdg.pro end ASSFIL: file /home/schwitrs/xplor/toppar/topallhdg.pro opened. RTFRDR>remark file topallhdg.pro RTFRDR>remark geometric energy function topology for distance geometry and RTFRDR>remark simulated annealing. RTFRDR>remark RTFRDR>remark history: RTFRDR>remark RTFRDR>remark XPLOR topology file TOPALLHSA.PRO, all hydrogens, RTFRDR>remark for simulated annealing, to be used with PARALLHSA.PRO RTFRDR>remark based on TOPALLH6.PRO. RTFRDR>remark internal coordinates from TOPH19.PRO. RTFRDR> RTFRDR>! all dihedrals defining planarity have been converted to impropers, RTFRDR>! the only dihedrals left are around rotatable bonds. RTFRDR>! some additional impropers were included in the rings to define planarity RTFRDR>! better. patches are included to define chirality at stereospecifically RTFRDR>! assigned prochiral centres and convert from trans to cis peptide bond. RTFRDR>! modifications by M. Nilges and P. Kraulis. RTFRDR>! added stereospecific impropers for all pro-chiral centers (ATB) RTFRDR> RTFRDR> RTFRDR>set message off echo off end RTFRDR> end X-PLOR> X-PLOR>segment SEGMENT> name=" " SEGMENT> chain CHAIN> LINK PEPP HEAD - * TAIL + PRO END { LINK to PRO } CHAIN> LINK PEPT HEAD - * TAIL + * END CHAIN> FIRSt PROP TAIL + PRO END { nter for PRO } CHAIN> FIRSt NTER TAIL + * END CHAIN> LAST CTER HEAD - * END CHAIN> sequence ala ala ala ala ala MAPIC: Atom numbers being modified SEQUence-element (terminate with END) = ala ala ala ala ala SEQUence-element (terminate with END) = end MAPIC: Atom numbers being modified CHAIN>end SEGMENT>end SEGMNT: 10 residues were inserted into segment " " XPLOR: current counts (number in parenthesis is maximum) NATOM= 103(MAXA= 200) NBOND= 102(MAXB= 200) NTHETA= 183(MAXT= 200) NGRP= 12(MAXGRP= 100) NPHI= 0(MAXP= 0) NIMPHI= 49(MAXIMP= 100) NDON= 0(MAXPAD= 0) NACC= 0(MAXPAD= 0) NNB= 0(MAXNB= 0) X-PLOR> X-PLOR>parameter PARRDR> @TOPPAR:parallhdg.pro ASSFIL: file /home/schwitrs/xplor/toppar/parallhdg.pro opened. PARRDR>remark file parallhdg.pro PARRDR>remark NOTE: these parameters are DEPRECATED. Please instead use protein.par. PARRDR>remark geometric energy function parameters for distance geometry and PARRDR>remark simulated annealing. PARRDR> PARRDR>set message off echo off end PARRDR> nbonds repel = 0.8 end PARRDR>end X-PLOR> X-PLOR>set seed = 8787380 end X-PLOR> X-PLOR>noe NOE> assign ( resid 1 and name ca ) ( resid 9 and name ca ) 5. 0.01 0.01 SELRPN: 1 atoms have been selected out of 103 SELRPN: 1 atoms have been selected out of 103 NOE>end X-PLOR> X-PLOR>flags include noe end X-PLOR> X-PLOR>mmdg MMDG> iacc=0.2 tacc=0.2 bacc=0.001 pacc=0.2 MMDG> writebounds=dgtest4.dat ASSFIL: file /home/schwitrs/xplor/test/dgtest4.dat opened. MMDG>end DGSMOOT: number of connections: 1070 DGSMOOT: using sparse matrix bound smoothing algorithm. DGSMOOT: max. size of network (upper, lower): 30 25 MMDG: writing smoothed bounds matrices to binary file. No metrization or embedding performed. X-PLOR>mmdg MMDG> readbounds=dgtest4.dat ASSFIL: file /home/schwitrs/xplor/test/dgtest4.dat opened. MMDG>end MMDG: no atoms will be metrized. DGSETNX: found 570 exclusions (1--2, 1--3) for repulsive lower bounds. 1 HA 1 CB 2.1270 2.1310 2.1430 * 2 HA 2 CB 2.1270 2.1394 2.1430 * 3 HA 3 CB 2.1270 2.1424 2.1430 * 4 HA 4 CB 2.1270 2.1394 2.1430 * 5 HA 5 CB 2.1270 2.1427 2.1430 * 6 HA 6 CB 2.1270 2.1378 2.1430 * 7 HA 7 CB 2.1270 2.1398 2.1430 * 8 HA 8 CB 2.1270 2.1333 2.1430 * 9 HA 9 CB 2.1270 2.1369 2.1430 * 10 HA 10 CB 2.1270 2.1318 2.1430 * * Geometric inconsistency--lower bound greater than upper. Attempted to continue by inverting these bounds. %DISGEO-ERR: There are geometric inconsistencies. Proceed at own risk. X-PLOR> X-PLOR>display $embedded TRUE X-PLOR>display $non_met_gap 9.03687 X-PLOR>display $dgscale 0.915828 X-PLOR> X-PLOR>coor copy end COOR: selected main coordinates copied to comp X-PLOR> X-PLOR>mmdg MMDG> readbounds=dgtest4.dat MMDG> storebounds MMDG> selection=( all ) SELRPN: 103 atoms have been selected out of 103 MMDG> scale=0.1 exponent=2 MMDG>end MMDG: storing smoothed bounds matrix in memory. No metrization or embedding performed. X-PLOR> X-PLOR>flags exclude * include dg end X-PLOR> X-PLOR>test first selection= ( resid 9 and name ca ) SELRPN: 1 atoms have been selected out of 103 TEST-FIRST> step=0.000001 tol=0.0 end EMMDG-info: vdw bounds are added to stored bounds matrix! DGSETNX: found 570 exclusions (1--2, 1--3) for repulsive lower bounds. TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 85 X ( 9 ALA CA ) 0.535724 0.535724 0.000000 85 Y ( 9 ALA CA ) 1.452053 1.452053 0.000000 85 Z ( 9 ALA CA ) 6.651721 6.651721 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>minimize powell nstep=200 drop=10. nprint=100 tolg=0. end POWELL: number of degrees of freedom= 309 --------------- cycle= 100 ------ stepsize= -0.0311 ----------------------- | Etotal =0.011 grad(E)=0.001 E(DG )=0.011 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= -0.4273 ----------------------- | Etotal =0.003 grad(E)=0.000 E(DG )=0.003 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>test first selection= ( resid 7 and name O ) step=0.000001 tol=0.0 end SELRPN: 1 atoms have been selected out of 103 TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 72 X ( 7 ALA O ) 0.000094 0.000094 0.000000 72 Y ( 7 ALA O ) 0.000242 0.000242 0.000000 72 Z ( 7 ALA O ) 0.000626 0.000626 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>flags exclude * include bonds angles impr dihe vdw noe end X-PLOR>constraints interaction=( all )=( all ) weights * 0.0001 end end SELRPN: 103 atoms have been selected out of 103 SELRPN: 103 atoms have been selected out of 103 X-PLOR>energy end MAKINB: mode 5 found 534 exclusions, 249 interactions(1-4) and 285 GB exclusions --------------- cycle= 1 -------------------------------------------------- | Etotal =2.872 grad(E)=0.070 E(BOND)=0.001 E(ANGL)=0.007 | | E(DIHE)=0.000 E(IMPR)=2.853 E(VDW )=0.007 E(NOE )=0.004 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>coor swap end COOR: selected coordinates swaped (main<->comp) X-PLOR> X-PLOR>mmdg MMDG> readbounds=dgtest4.dat MMDG> storebounds MMDG> selection=( name ca or name n or name c ) SELRPN: 30 atoms have been selected out of 103 MMDG> scale=0.1 exponent=2 MMDG>end MMDG: storing smoothed bounds matrix in memory. No metrization or embedding performed. X-PLOR> X-PLOR>flags exclude * include dg end X-PLOR> X-PLOR>test first selection= ( resid 9 and name ca ) SELRPN: 1 atoms have been selected out of 103 TEST-FIRST> step=0.000001 tol=0.0 end EMMDG-info: vdw bounds are added to stored bounds matrix! DGSETNX: found 570 exclusions (1--2, 1--3) for repulsive lower bounds. TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 85 X ( 9 ALA CA ) 0.555058 0.555058 0.000000 85 Y ( 9 ALA CA ) 0.684923 0.684923 0.000000 85 Z ( 9 ALA CA ) 2.717146 2.717146 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>minimize powell nstep=200 drop=10. nprint=100 tolg=0. end POWELL: number of degrees of freedom= 309 --------------- cycle= 100 ------ stepsize= 0.1165 ----------------------- | Etotal =0.000 grad(E)=0.000 E(DG )=0.000 | ------------------------------------------------------------------------------- --------------- cycle= 200 ------ stepsize= 0.2055 ----------------------- | Etotal =0.000 grad(E)=0.000 E(DG )=0.000 | ------------------------------------------------------------------------------- POWELL: STEP number limit. Normal termination POWELL: Current coordinates set to last minimum X-PLOR> X-PLOR>test first selection= ( resid 7 and name O ) step=0.000001 tol=0.0 end SELRPN: 1 atoms have been selected out of 103 TESTFD: Parameters: STEP= 0.00000 MASSweighting=F TESTFD: The following first derivatives differ by more than TOL= 0.000000 DIM. ATOM ANALYTIC FINITE-DIFF DEVIATION 72 X ( 7 ALA O ) 0.000000 0.000000 0.000000 72 Y ( 7 ALA O ) 0.000000 0.000000 0.000000 72 Z ( 7 ALA O ) 0.000000 0.000000 0.000000 TESTFD: A total of 0 elements were within the tolerance X-PLOR> X-PLOR>flags exclude * include bonds angles impr dihe vdw noe end X-PLOR>constraints interaction=( name ca or name n or name c )=( prev ) SELRPN: 30 atoms have been selected out of 103 SELRPN: 30 atoms have been selected out of 103 CONS> weights * 0.0001 end end X-PLOR> X-PLOR>energy end MAKINB: mode 5 found 84 exclusions, 27 interactions(1-4) and 57 GB exclusions --------------- cycle= 2 -------------------------------------------------- | Etotal =0.027 grad(E)=0.023 E(BOND)=0.000 E(ANGL)=0.000 | | E(DIHE)=0.000 E(IMPR)=0.026 E(VDW )=0.000 E(NOE )=0.001 | ------------------------------------------------------------------------------- X-PLOR> X-PLOR>stop HEAP: maximum use= 633514 current use= 598985 X-PLOR: total CPU time= 0.2000 s X-PLOR: entry time at 16:37:38 22-Feb-07 X-PLOR: exit time at 16:37:39 22-Feb-07