Dear Xplor users, I am facing the xplor instability during the PASD procedure. The structure generating steps (sa_pass2.tcl, sa_pass3.tcl) are killed before the full number of structures is generated.
the last message in the file is: /usr/local/chem/xplor-nih-2.24/bin/xplor: line 471: 1308 Killed /usr/local/chem/xplor-nih-2.24/bin.Linux_2.6_x86_64/xplor '-tcl' 'sa_pass2.tcl' The output file is attached (only beginning and the end of file to decrease the size) . There is no difference if the procedure run on single processor or on multiple processors (via the "-smp" flag). the processors are: Intel Xeon E5430 2.66GHz operating system: mandriva 2008.1 x86_64 There is no problem with other structure calculation protocols with low number of generated structures required (e.g. UNIO with 80 structures/iteration) though. there should not be the problem with limits. ulimit -a output: on server: core file size (blocks, -c) 0 data seg size (kbytes, -d) unlimited scheduling priority (-e) 20 file size (blocks, -f) unlimited pending signals (-i) 71680 max locked memory (kbytes, -l) 32 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) 8192 cpu time (seconds, -t) unlimited max user processes (-u) 71680 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited on client: core file size (blocks, -c) unlimited data seg size (kbytes, -d) unlimited scheduling priority (-e) 0 file size (blocks, -f) unlimited pending signals (-i) 38912 max locked memory (kbytes, -l) 32 max memory size (kbytes, -m) unlimited open files (-n) 1024 pipe size (512 bytes, -p) 8 POSIX message queues (bytes, -q) 819200 real-time priority (-r) 0 stack size (kbytes, -s) unlimited cpu time (seconds, -t) unlimited max user processes (-u) 38912 virtual memory (kbytes, -v) unlimited file locks (-x) unlimited the xplor script is also included in attachment. Any help would be greatly appreciated. Thank you in advance. Best regards Pavel -- MPharm.Pavel Macek,Ph.D. Institute of Microbiology, v.v.i. Academy of Sciences of the Czech Republic E-mail:[email protected] Tel.:(+420) 608 434339
XPLOR-NIH version 2.24 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: macek on: bb01 (x86_64/Linux ) at: 10-Jun-10 04:28:21 TCL># TCL># cyanovirin test TCL># TCL> TCL>package require marvin [Server accepting clients] [Connect from bb01 (process 5)] [Connect from bb01 (process 3)] [Connect from bb01 (process 7)] [Connect from bb01 (process 2)] [Connect from bb01 (process 1)] [Connect from bb01 (process 6)] [Connect from bb01 (process 4)] 1.0 TCL> TCL># TCL># this entire example takes about 12 hours to run on a 60-processor cluster. TCL># If you just want to verify that things run, run all the scripts with TCL># the flag -quick TCL># TCL> TCL>set quickMode [flagExists $argv -quick] 0 TCL> TCL># TCL># initialization TCL># TCL> TCL>initParamPsfPdb \ TCL> -psfFileName ./spm177.psf \ TCL> -randomCoords X-PLOR>param @/usr/local/chem/xplor-nih-2.24/toppar/protein.par end ASSFIL: file /usr/local/chem/xplor-nih-2.24/toppar/protein.par opened. PARRDR>! PARRDR>! xplor-nih protein parameter file, version 1.0 PARRDR>! PARRDR>! This file is intended to work with the topology file protein-1.0.top PARRDR>! PARRDR>! This is a re-named copy of the file parallhdg_procheck.pro PARRDR>! PARRDR>! We've created this new filename in order to eliminate confusion PARRDR>! between the various parameter/topology combinations that ship PARRDR>! with xplor-nih. It has version numbers, and will be updated PARRDR>! along with the rest of the xplor-nih package. PARRDR>! PARRDR>! Its backbone bond lengths and angles are designed to agree with PARRDR>! the Engh & Huber parameter set (reference below), which is used by PARRDR>! PROCHECK, among other structure-validation programs. PARRDR>! PARRDR>! If you find errors, PLEASE let us know. PARRDR>! PARRDR> PARRDR> PARRDR> PARRDR> PARRDR>remark file protein-1.0.par PARRDR>remark Changed version of parallhdg_new.pro so that the bond lengths and angles PARRDR>remark agree with what PROCHECK expects. PARRDR>remark JJK 9/14/98 PARRDR> PARRDR>! file parallhdg_new.pro PARRDR>! geometric energy function parameters for distance geometry and PARRDR>! simulated annealing. Modified by G.M.C. to have sigma's of Param19x and parafloat PARRDR> PARRDR>set message off echo off end PARRDR> end X-PLOR>end X-PLOR>struct @./spm177.psf end ASSFIL: file /scratch/macek/spm177.420/./spm177.psf opened. STRUcture>PSF REMARKS FILENAME="/home/pavelm/scratch/SPMcalc/Calc/SPM177.psf" REMARKS TOPH11-MACRO for protein sequence REMARKS DATE:12-Feb-10 13:36:29 created by user: pavelm XPLOR: current counts (number in parenthesis is maximum) NATOM= 2589(MAXA= 3200) NBOND= 2605(MAXB= 3200) NTHETA= 4681(MAXT= 6400) NGRP= 1081(MAXGRP= 1600) NPHI= 284(MAXP= 400) NIMPHI= 1350(MAXIMP= 1600) NDON= 0(MAXPAD= 100) NACC= 0(MAXPAD= 100) NNB= 1068(MAXNB= 1600) STRUcture> end X-PLOR>end X-PLOR>vector do (mass = 100.0) (all) SELRPN: 2589 atoms have been selected out of 2589 X-PLOR>end TCL> TCL># TCL># quick mode will only calculate the structure of the first 36 residues of cyanovirin TCL># TCL> TCL>if {$quickMode} { TCL> XplorCommand "delete sele (not (resid 1:36)) end" TCL>} TCL> TCL># TCL># make sure the initial coords have good covalent geometry TCL># TCL> TCL>cleanCovalentGeom X-PLOR>set message off echo off print off end X-PLOR>end TCL> TCL> TCL># TCL># set up the 3dC NOEs TCL># TCL> TCL>XplorCommand "set message off echo off end" X-PLOR>set message off echo off end TCL> TCL>set noe_3dc [create_MarvinNOEPotential 3dC] _d0dad60100000000_p_rc_DerivedPotTMarvinNOEPotential_t TCL> TCL>readShiftAssignments \ TCL> -fileName "spm177_3dc_pass2.shiftAssignments" \ TCL> -pot $noe_3dc TCL> TCL>readMarvinPeaks \ TCL> -fileName "spm177_3dc_pass2.peaks" \ TCL> -pot $noe_3dc TCL> TCL>readExplicitInverseExceptions \ TCL> -fileName "spm177_3dc.exceptions" \ TCL> -pot $noe_3dc TCL> TCL> TCL># TCL># set up the 3dN NOEs TCL># TCL> TCL>XplorCommand "set message off echo off end" TCL> TCL>set noe_3dn [create_MarvinNOEPotential 3dN] _f0eb810300000000_p_rc_DerivedPotTMarvinNOEPotential_t TCL> TCL>readShiftAssignments \ TCL> -fileName "spm177_3dn_pass2.shiftAssignments" \ TCL> -pot $noe_3dn TCL> TCL>readMarvinPeaks \ TCL> -fileName "spm177_3dn_pass2.peaks" \ TCL> -pot $noe_3dn TCL> TCL>readExplicitInverseExceptions \ TCL> -fileName "spm177_3dn.exceptions" \ TCL> -pot $noe_3dn TCL> TCL> TCL> TCL># TCL># set up the TALOS restraints TCL># TCL> TCL>set talos [create_XplorPot CDIH] _9050070400000000_p_rc_DerivedPotTXplorPot_t TCL> TCL>if {$quickMode} { TCL> TCL> readIndividualResidueTalos -fileNames [list \ TCL> ./talos/pred/res004.tab \ TCL> ./talos/pred/res007.tab \ TCL> ./talos/pred/res008.tab \ TCL> ./talos/pred/res009.tab \ TCL> ./talos/pred/res012.tab \ TCL> ./talos/pred/res013.tab \ TCL> ./talos/pred/res014.tab \ TCL> ./talos/pred/res015.tab \ TCL> ./talos/pred/res017.tab \ TCL> ./talos/pred/res018.tab \ TCL> ./talos/pred/res019.tab \ TCL> ./talos/pred/res020.tab \ TCL> ./talos/pred/res021.tab \ TCL> ./talos/pred/res022.tab \ TCL> ./talos/pred/res023.tab \ TCL> ./talos/pred/res024.tab \ TCL> ./talos/pred/res025.tab \ TCL> ./talos/pred/res026.tab \ TCL> ./talos/pred/res029.tab \ TCL> ./talos/pred/res030.tab \ TCL> ./talos/pred/res031.tab \ TCL> ./talos/pred/res033.tab \ TCL> ./talos/pred/res034.tab \ TCL> ./talos/pred/res035.tab] TCL> TCL>} else { TCL> readIndividualResidueTalos -fileNames [glob ./talos/pred/*tab] TCL>} 63 74.184 15.218499999999999 30.735 48.0725 117 -62.236999999999995 -30.403 23.718 20.0 150 -147.536 133.2635 32.650000000000006 20.0 154 -117.96799999999999 128.716 35.293 22.400000000000006 139 -111.231 99.99199999999999 60.07599999999999 68.609 11 -102.5685 115.68100000000001 51.4435 23.083000000000006 73 -118.5275 141.94 51.9305 26.954 54 -193.77450000000002 146.2965 109.9915 41.9835 170 -111.9145 118.23150000000001 44.1395 49.21150000000001 160 -131.365 157.973 22.055999999999997 20.0 135 -129.414 140.81 23.352999999999994 41.056000000000004 134 -123.867 155.1775 41.283 20.0 6 -73.85900000000001 -25.4785 25.96 28.9145 121 -87.94900000000001 175.6405 21.927 20.0 82 -71.5745 -29.573 20.0 22.961999999999996 151 -126.274 130.223 34.245000000000005 20.0 65 -129.1935 155.928 39.6465 20.0 109 -78.7835 -15.314 29.659499999999998 28.631 127 -88.844 122.82249999999999 37.689 40.7015 41 -76.5 -26.791 24.798000000000002 23.983 145 -36.6605 120.1465 123.9105 49.1405 138 -93.562 -6.6229999999999976 33.997 34.906000000000006 75 -73.0755 -26.616500000000002 27.1535 33.1085 86 -72.5185 -32.6215 33.204499999999996 20.0 62 -67.618 144.8135 21.534 22.360500000000002 162 -109.81700000000001 161.4745 63.018 28.992500000000007 39 -95.2215 135.216 38.7735 27.197000000000003 9 -168.299 132.472 114.451 37.297000000000004 106 -112.85 132.3145 30.476999999999997 25.5435 105 -122.67250000000001 121.372 28.6625 25.644999999999996 49 -71.3675 -19.896 32.0535 32.797 99 -63.16499999999999 -43.748999999999995 20.0 20.0 136 -74.0715 133.9685 20.0 20.0 94 -67.37 -8.5685 20.0 35.4495 50 -90.714 7.2645 24.075000000000003 20.1615 153 -141.178 154.176 20.589 20.0 71 91.701 -0.09950000000000259 20.0 25.1545 161 -143.971 164.483 26.969 29.933999999999997 5 -102.488 193.005 49.638000000000005 94.45400000000001 164 -165.71750000000003 153.73250000000002 127.84350000000002 33.173500000000004 100 -74.131 -21.167499999999997 22.206000000000003 21.8215 4 -127.3655 159.18400000000003 46.505500000000005 31.283 155 -96.7625 164.1335 40.7505 21.53049999999999 149 -127.5415 151.344 35.909499999999994 29.708 69 -66.372 -17.354 20.162000000000003 30.255000000000003 44 -123.5195 151.633 39.2725 36.647 83 -67.523 -32.772999999999996 22.692999999999998 20.0 125 -91.463 -9.1815 29.35 22.4375 68 -99.56649999999999 132.292 39.527499999999996 43.163999999999994 3 -141.723 152.7835 28.32 26.186499999999995 47 -139.55100000000002 137.3915 25.749000000000002 23.871500000000005 131 -37.096500000000006 176.846 92.6725 66.118 66 -102.10400000000001 130.9355 51.464000000000006 20.0 133 -113.7175 3.9045000000000023 35.7095 24.378500000000003 156 -60.386 -25.8185 20.0 23.694499999999998 12 -104.745 117.1825 39.373 35.714499999999994 55 -100.0205 118.5255 23.735500000000002 38.8655 76 -116.12549999999999 -0.7250000000000014 38.4505 20.055 148 -38.00750000000001 -175.4805 113.8755 104.61149999999999 152 -131.6665 146.97750000000002 44.80650000000001 23.284499999999994 78 -70.6975 -41.429 20.0 20.0 146 -121.94399999999999 126.53399999999999 39.269 20.0 118 -89.44749999999999 -14.637999999999998 36.5255 45.401 128 -92.2905 -16.0405 23.7175 39.7705 7 -94.0645 8.8495 27.4255 21.7465 8 77.203 20.854999999999997 43.894 36.306 53 88.84049999999999 -8.581499999999998 20.0 21.250500000000002 97 -67.97 -31.633000000000003 20.0 27.58 96 -88.991 -5.022999999999996 39.128 44.31 116 -62.203500000000005 -33.801 20.0 29.819 43 -115.49449999999999 137.3365 55.3135 32.88550000000001 101 -75.146 -22.124499999999998 22.224000000000004 37.914500000000004 115 -59.623999999999995 -24.566 20.0 30.822 122 -58.241 -31.54 20.0 20.0 81 -65.593 -38.2575 20.0 20.0 79 -63.0065 -43.5055 20.0 20.0 137 -88.035 -19.463500000000003 34.646 39.4045 110 -96.896 -32.861 30.634 32.347 89 -100.295 7.248999999999999 33.968 32.677 166 -108.54400000000001 134.9125 35.154 26.676499999999997 124 -67.4125 -39.656499999999994 20.0 20.0 48 -120.0495 126.8055 56.5105 23.8375 147 -107.131 115.78 29.068999999999996 25.159999999999997 45 -101.46700000000001 134.6005 34.86300000000001 24.8455 61 -126.9615 134.487 53.573499999999996 33.513 120 -133.2045 151.0 23.551499999999997 30.502000000000002 98 -86.3885 -12.899000000000001 37.2415 45.149 77 65.37299999999999 25.218000000000004 32.064 28.321 13 -123.31700000000001 166.0275 22.6 27.384500000000003 123 -64.5715 -38.937 20.0 20.0 90 -86.36850000000001 -31.782000000000004 21.8375 26.604 103 -126.345 141.55599999999998 25.607 29.965999999999994 14 -177.2175 172.86 52.051500000000004 27.80900000000001 119 -132.299 127.6265 48.236 26.652499999999996 64 -115.476 178.666 43.80799999999999 109.74600000000001 130 -119.115 142.3925 54.340999999999994 26.2455 70 -90.714 4.760499999999999 24.075000000000003 20.0 2 -110.8835 136.389 52.24449999999999 30.406999999999996 158 82.5465 15.141499999999997 26.854499999999998 40.3955 84 -90.226 -22.2115 37.304 42.9965 157 -87.99199999999999 -8.271999999999998 20.576 22.242 132 -82.0005 -19.978500000000004 35.9025 38.8895 72 -106.60050000000001 117.6885 31.8285 56.6805 51 54.567499999999995 35.2865 24.6825 24.7995 74 -130.813 148.81900000000002 67.936 34.519999999999996 40 -62.96 -31.7545 20.0 24.6545 163 -136.55100000000002 153.13299999999998 23.255000000000003 20.0 80 -61.7915 -40.346000000000004 20.0 20.0 107 -85.15799999999999 114.9445 24.085 28.554499999999997 88 68.7015 26.928 35.3925 26.611 129 -132.4005 172.038 47.6955 29.299999999999997 104 -137.09300000000002 133.36950000000002 34.093 21.454500000000003 169 -99.2445 139.1215 45.5065 21.531499999999994 67 -116.993 118.794 26.438999999999993 25.76299999999999 10 207.064 -197.4855 81.595 40.283500000000004 38 -34.802499999999995 121.592 101.0365 31.908 168 -101.673 128.2135 43.078 27.6545 167 -100.339 126.4765 20.0 26.5295 91 -137.0685 147.0085 29.292499999999997 20.0 42 -113.167 139.7 44.97 28.500999999999998 92 -102.215 120.9995 24.476999999999997 25.5955 52 -102.755 1.6555 31.964 20.0 159 -101.123 160.463 43.062 20.445999999999998 126 86.7645 16.746999999999996 41.3265 42.001 60 -75.626 -20.6235 30.030000000000005 30.1505 165 -110.684 137.83249999999998 49.87200000000001 30.980499999999992 93 -103.7545 155.3835 50.5945 46.637499999999996 46 -135.9105 153.68 20.0 27.433999999999997 85 -116.93549999999999 90.815 54.3715 59.432 87 -95.8905 13.1185 20.0 20.0 102 -159.317 191.5045 123.43299999999999 96.3295 108 -62.92400000000001 -19.647 23.610000000000003 32.548 95 -79.0215 -23.770999999999997 26.550500000000003 27.523 114 -91.5155 117.7525 30.442500000000003 35.149499999999996 %CSTRAN: allocating space for 268 assignments. TCL> TCL> TCL># TCL># set up the DELPHIC terms TCL># TCL> TCL>setupDelphicTorsions X-PLOR>end X-PLOR>@GAUSSIANS:newshortrange_setup.tbl ASSFIL: file /usr/local/chem/xplor-nih-2.24/databases/torsions_gaussians/newshortrange_setup.tbl opened. X-PLOR>! X-PLOR>! setup.tbl X-PLOR>! Sets up the selections for the various database energies X-PLOR>! Works with all.tbl X-PLOR>! X-PLOR>! WARNING: this script overwrites the store4, store5, and store6 arrays X-PLOR>! X-PLOR>! by John Kuszewski 6/19/96 X-PLOR>! modified from earlier version for PROCHECK database energy X-PLOR>! X-PLOR>! modified 11/17/96 JJK for new phi/psi/chi1 dists X-PLOR>! modified 9/15/97 JJK for new residue-specific dists X-PLOR>! X-PLOR> X-PLOR>! X-PLOR>! select the Cas of the residues you want to apply intraresidue TA database X-PLOR>! assignments to here X-PLOR>! X-PLOR> X-PLOR>vector identify (store4) (all) SELRPN: 2589 atoms have been selected out of 2589 X-PLOR> X-PLOR>! X-PLOR>! the user has to change this selection statement so that X-PLOR>! store5 selects all cis-proline residues! X-PLOR>! X-PLOR> X-PLOR>vector identify (store5) (resn cisp) SELRPN: 0 atoms have been selected out of 2589 X-PLOR> X-PLOR>set message off echo off end X-PLOR>end TCL>set deltorPot [create_XplorPot RAMA] _9054070400000000_p_rc_DerivedPotTXplorPot_t TCL> TCL># TCL># handle IVM setup TCL># TCL> TCL>setupIVM \ TCL> -toleranceMultiplier 100.0 TCL> TCL> TCL># TCL># remarks to tack onto each PDB file TCL># TCL> TCL> TCL>set remList [list] TCL> TCL>if {$quickMode} { TCL> set nStructs 20 TCL>} else { TCL> set nStructs 800 TCL>} 800 TCL> TCL>pass2 \ TCL> -numStructs $nStructs \ TCL> -outFilenameTemplate "spm177_pass2_%d.pdb" \ TCL> -remarksList $remList \ TCL> -potsToUseDuringRandomization [list $talos] \ TCL> -potsToUseDuringAnnealing [list $noe_3dc $noe_3dn $talos $deltorPot] \ TCL> -noePot [list $noe_3dc $noe_3dn] \ TCL> -completeNoePot [list $noe_3dc $noe_3dn] \ TCL> -randomSeed 42 beginning of calculation of structure number 0 X-PLOR>set message off echo off print off end X-PLOR>end !!! !!! calulation running here !!! cooling cycle 37 of 156 X-PLOR>param nbonds repel 0.8750480620246555 rcon 0.1200823963820805 end end X-PLOR>end X-PLOR>rama scale 0.3002059909552013 end X-PLOR>end X-PLOR>restraints dihed scale 200.0 end X-PLOR>end MAKINB: mode 4 found 14414 exclusions, 0 interactions(1-4) and 7892 GB exclusions *--- Dynamics ---- step= 0 ---- time= 0 ---- delta_t= 0.0061393 --* | E(kin)+E(poten)= 23082.869 E(kin)= 2274.297 temperature= 2919.588 | | E(poten)= 20808.5717800 grad= 14.3744594 3dC= 13275.0406428 | | 3dN= 5731.4666827 ANGL= 133.0055173 BOND= 0.8649922 | | CDIH= 411.8539250 IMPR= 13.7047160 RAMA= -169.2112144 | | VDW= 1411.8465184 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 10 ---- time= 0.062378 ---- delta_t= 0.0064765 --* | E(kin)+E(poten)= 23111.182 E(kin)= 2326.094 temperature= 2986.081 | | E(poten)= 20785.0884545 grad= 14.7704604 3dC= 13256.1767265 | | 3dN= 5718.2925922 ANGL= 131.0949483 BOND= 0.9506170 | | CDIH= 430.6246882 IMPR= 12.7926239 RAMA= -174.0058312 | | VDW= 1409.1620897 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 20 ---- time= 0.13067 ---- delta_t= 0.00699 --* | E(kin)+E(poten)= 23061.389 E(kin)= 2392.276 temperature= 3071.041 | | E(poten)= 20669.1123481 grad= 14.5211942 3dC= 13242.4808515 | | 3dN= 5693.1845427 ANGL= 135.0872233 BOND= 1.7771505 | | CDIH= 378.7540744 IMPR= 16.1084409 RAMA= -177.4070481 | | VDW= 1379.1271129 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 30 ---- time= 0.1993 ---- delta_t= 0.0069978 --* | E(kin)+E(poten)= 22982.542 E(kin)= 2376.201 temperature= 3050.405 | | E(poten)= 20606.3414172 grad= 14.4220439 3dC= 13244.0288972 | | 3dN= 5675.2592614 ANGL= 131.7709141 BOND= 1.9606191 | | CDIH= 360.8598620 IMPR= 12.5551336 RAMA= -177.0211362 | | VDW= 1356.9278661 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 40 ---- time= 0.26827 ---- delta_t= 0.0070847 --* | E(kin)+E(poten)= 22943.871 E(kin)= 2393.239 temperature= 3072.277 | | E(poten)= 20550.6318230 grad= 13.2224523 3dC= 13252.4114922 | | 3dN= 5669.1870405 ANGL= 119.9019844 BOND= 0.9156336 | | CDIH= 338.6036066 IMPR= 10.4678968 RAMA= -173.8011288 | | VDW= 1332.9452976 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 50 ---- time= 0.3389 ---- delta_t= 0.0070599 --* | E(kin)+E(poten)= 22903.185 E(kin)= 2404.436 temperature= 3086.652 | | E(poten)= 20498.7482860 grad= 11.6240298 3dC= 13259.8940206 | | 3dN= 5659.8993453 ANGL= 97.1057170 BOND= 1.2498893 | | CDIH= 329.1061441 IMPR= 10.3090288 RAMA= -170.8270558 | | VDW= 1312.0111967 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 60 ---- time= 0.40969 ---- delta_t= 0.0067686 --* | E(kin)+E(poten)= 22886.049 E(kin)= 2412.496 temperature= 3096.998 | | E(poten)= 20473.5524557 grad= 10.9068528 3dC= 13257.5136995 | | 3dN= 5642.9264203 ANGL= 85.7302128 BOND= 1.2170394 | | CDIH= 337.8272714 IMPR= 5.9829778 RAMA= -168.7743535 | | VDW= 1311.1291880 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 70 ---- time= 0.47733 ---- delta_t= 0.0064896 --* | E(kin)+E(poten)= 22883.654 E(kin)= 2394.168 temperature= 3073.470 | | E(poten)= 20489.4855411 grad= 11.5321099 3dC= 13233.3682744 | | 3dN= 5622.6858048 ANGL= 89.4643421 BOND= 0.8036390 | | CDIH= 363.1238668 IMPR= 5.9594582 RAMA= -164.7852960 | | VDW= 1338.8654517 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 80 ---- time= 0.54389 ---- delta_t= 0.0064712 --* | E(kin)+E(poten)= 22914.439 E(kin)= 2392.880 temperature= 3071.816 | | E(poten)= 20521.5595385 grad= 12.6906600 3dC= 13193.6482454 | | 3dN= 5608.4481080 ANGL= 93.9528201 BOND= 0.8861232 | | CDIH= 409.8398359 IMPR= 5.6622010 RAMA= -161.0040599 | | VDW= 1370.1262647 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 90 ---- time= 0.61083 ---- delta_t= 0.0063985 --* | E(kin)+E(poten)= 22884.010 E(kin)= 2409.324 temperature= 3092.926 | | E(poten)= 20474.6865759 grad= 11.9351970 3dC= 13160.2454945 | | 3dN= 5612.4033078 ANGL= 103.7975537 BOND= 0.9249342 | | CDIH= 361.6846440 IMPR= 6.3756740 RAMA= -158.9120492 | | VDW= 1388.1670169 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 100 ---- time= 0.67756 ---- delta_t= 0.0065382 --* | E(kin)+E(poten)= 22863.338 E(kin)= 2370.722 temperature= 3043.371 | | E(poten)= 20492.6163764 grad= 12.0763964 3dC= 13149.7851833 | | 3dN= 5624.1970721 ANGL= 109.5979252 BOND= 3.4189749 | | CDIH= 356.9289610 IMPR= 8.4124104 RAMA= -158.2429811 | | VDW= 1398.5188305 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 110 ---- time= 0.74411 ---- delta_t= 0.0066634 --* | E(kin)+E(poten)= 22918.138 E(kin)= 2348.347 temperature= 3014.648 | | E(poten)= 20569.7909258 grad= 13.3946305 3dC= 13140.7590929 | | 3dN= 5631.7511335 ANGL= 115.4756093 BOND= 5.2095294 | | CDIH= 411.3943569 IMPR= 6.8099689 RAMA= -160.6864197 | | VDW= 1419.0776546 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 120 ---- time= 0.81116 ---- delta_t= 0.0065542 --* | E(kin)+E(poten)= 22973.927 E(kin)= 2352.396 temperature= 3019.845 | | E(poten)= 20621.5316775 grad= 14.7559549 3dC= 13134.3597096 | | 3dN= 5630.8758362 ANGL= 128.5937035 BOND= 3.0846800 | | CDIH= 438.9718007 IMPR= 8.2338324 RAMA= -165.7290783 | | VDW= 1443.1411934 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 130 ---- time= 0.87764 ---- delta_t= 0.0065034 --* | E(kin)+E(poten)= 22974.924 E(kin)= 2363.629 temperature= 3034.266 | | E(poten)= 20611.2947610 grad= 14.7557251 3dC= 13145.8886749 | | 3dN= 5620.9902092 ANGL= 137.7413875 BOND= 1.2809235 | | CDIH= 403.6641951 IMPR= 14.0369046 RAMA= -170.7650543 | | VDW= 1458.4575204 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 140 ---- time= 0.94268 ---- delta_t= 0.006385 --* | E(kin)+E(poten)= 22956.709 E(kin)= 2356.954 temperature= 3025.697 | | E(poten)= 20599.7544647 grad= 14.9307724 3dC= 13167.1630970 | | 3dN= 5606.0356458 ANGL= 143.7585295 BOND= 0.8346264 | | CDIH= 393.1045914 IMPR= 11.6120407 RAMA= -172.4594177 | | VDW= 1449.7053517 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 150 ---- time= 1.007 ---- delta_t= 0.0063463 --* | E(kin)+E(poten)= 22948.896 E(kin)= 2360.402 temperature= 3030.123 | | E(poten)= 20588.4941743 grad= 15.4405304 3dC= 13172.8728736 | | 3dN= 5585.8038597 ANGL= 142.1095592 BOND= 1.2160634 | | CDIH= 418.9152207 IMPR= 11.2637707 RAMA= -169.6023058 | | VDW= 1425.9151328 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 160 ---- time= 1.0715 ---- delta_t= 0.0064335 --* | E(kin)+E(poten)= 22909.092 E(kin)= 2378.699 temperature= 3053.611 | | E(poten)= 20530.3936854 grad= 15.4303751 3dC= 13160.8942936 | | 3dN= 5564.8018461 ANGL= 136.5572433 BOND= 3.9556028 | | CDIH= 421.1282151 IMPR= 12.3551182 RAMA= -165.4878257 | | VDW= 1396.1891920 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 170 ---- time= 1.1365 ---- delta_t= 0.0065743 --* | E(kin)+E(poten)= 22852.637 E(kin)= 2375.292 temperature= 3049.238 | | E(poten)= 20477.3448577 grad= 15.0328502 3dC= 13147.2425303 | | 3dN= 5557.2025524 ANGL= 136.4416951 BOND= 4.9734917 | | CDIH= 434.0143491 IMPR= 8.4068756 RAMA= -161.6727666 | | VDW= 1350.7361301 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 180 ---- time= 1.2024 ---- delta_t= 0.0064515 --* | E(kin)+E(poten)= 22844.668 E(kin)= 2347.531 temperature= 3013.600 | | E(poten)= 20497.1373857 grad= 15.2037712 3dC= 13156.3812584 | | 3dN= 5567.9485219 ANGL= 138.5581971 BOND= 2.9987916 | | CDIH= 481.8185621 IMPR= 10.5310496 RAMA= -159.2923752 | | VDW= 1298.1933803 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 190 ---- time= 1.2677 ---- delta_t= 0.0062497 --* | E(kin)+E(poten)= 22880.258 E(kin)= 2340.879 temperature= 3005.061 | | E(poten)= 20539.3793485 grad= 15.7826406 3dC= 13185.6854467 | | 3dN= 5589.8557406 ANGL= 142.7040427 BOND= 1.5904653 | | CDIH= 500.9930291 IMPR= 14.4106954 RAMA= -161.1254849 | | VDW= 1265.2654136 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 200 ---- time= 1.3316 ---- delta_t= 0.0064756 --* | E(kin)+E(poten)= 22866.573 E(kin)= 2373.014 temperature= 3046.314 | | E(poten)= 20493.5583391 grad= 14.8936791 3dC= 13215.0955759 | | 3dN= 5609.5585044 ANGL= 143.9673165 BOND= 1.1182256 | | CDIH= 444.9346767 IMPR= 10.1901143 RAMA= -163.0587368 | | VDW= 1231.7526625 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 210 ---- time= 1.3966 ---- delta_t= 0.0063868 --* | E(kin)+E(poten)= 22840.851 E(kin)= 2354.043 temperature= 3021.960 | | E(poten)= 20486.8079097 grad= 15.0451812 3dC= 13245.7868259 | | 3dN= 5624.8563443 ANGL= 141.1573157 BOND= 2.1055934 | | CDIH= 428.4290388 IMPR= 12.3307149 RAMA= -163.1075306 | | VDW= 1195.2496073 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 220 ---- time= 1.4612 ---- delta_t= 0.0065121 --* | E(kin)+E(poten)= 22856.043 E(kin)= 2350.758 temperature= 3017.743 | | E(poten)= 20505.2847145 grad= 15.1372136 3dC= 13275.7907500 | | 3dN= 5641.3905181 ANGL= 137.9123030 BOND= 4.1215482 | | CDIH= 424.8551987 IMPR= 12.0944120 RAMA= -162.1825266 | | VDW= 1171.3025110 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 230 ---- time= 1.5261 ---- delta_t= 0.006471 --* | E(kin)+E(poten)= 22841.031 E(kin)= 2367.200 temperature= 3038.850 | | E(poten)= 20473.8307486 grad= 14.1293434 3dC= 13284.9620802 | | 3dN= 5657.7300248 ANGL= 142.2121114 BOND= 4.4320930 | | CDIH= 384.1151694 IMPR= 8.9841738 RAMA= -161.5326063 | | VDW= 1152.9277024 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 240 ---- time= 1.5916 ---- delta_t= 0.0064063 --* | E(kin)+E(poten)= 22849.556 E(kin)= 2338.026 temperature= 3001.399 | | E(poten)= 20511.5298560 grad= 14.4380323 3dC= 13274.4451986 | | 3dN= 5669.3666321 ANGL= 141.5002034 BOND= 3.6515939 | | CDIH= 424.5183884 IMPR= 12.7710939 RAMA= -162.0826270 | | VDW= 1147.3593728 | *------------------------------------------------------------------------------* *--- Dynamics ---- step= 242 ---- time= 1.6046 ---- delta_t= 0.0065103 --* | E(kin)+E(poten)= 22867.309 E(kin)= 2360.201 temperature= 3029.866 | | E(poten)= 20507.1077047 grad= 13.9652074 3dC= 13271.1901935 | | 3dN= 5670.8846500 ANGL= 130.7162116 BOND= 2.6456253 | | CDIH= 437.7626274 IMPR= 9.6320301 RAMA= -162.4833807 | | VDW= 1146.7597475 | *------------------------------------------------------------------------------* cooling cycle 38 of 156 X-PLOR>param nbonds repel 0.8743833738463508 rcon 0.12370366648119539 end end X-PLOR>end X-PLOR>rama scale 0.3092591662029885 end X-PLOR>end X-PLOR>restraints dihed scale 200.0 end X-PLOR>end /usr/local/chem/xplor-nih-2.24/bin/xplor: line 471: 1308 Killed /usr/local/chem/xplor-nih-2.24/bin.Linux_2.6_x86_64/xplor '-tcl' 'sa_pass2.tcl'
xplor
Description: application/shellscript
_______________________________________________ Xplor-nih mailing list [email protected] http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
