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:pav.macek at gmail.com
Tel.:(+420) 608 434339
-------------- next part --------------
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'
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