[gmx-users] g_rms Fatal error: Error: Too many iterations in routine JACOBI
Anthony Cruz
acb15885 at uprm.edu
Wed May 25 19:55:46 CEST 2005
I do the gmxcheck and this is the result:
Checking file 1scn_bx_w_fullMD_mv.trr
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000
# Atoms 110719
Last frame 10500 time 10500.001
Item #frames Timestep (ps)
Step 10501 1
Time 10501 1
Lambda 10501 1
Coords 10501 1
Velocities 10501 1
Forces 0
Box 10501 1
Checking coordinate file 1scn_bx_w_CL_TPR4fullMD.tpr
Reading file 1scn_bx_w_CL_TPR4fullMD.tpr, VERSION 3.2.1 (single precision)
Reading file 1scn_bx_w_CL_TPR4fullMD.tpr, VERSION 3.2.1 (single precision)
110719 atoms in file
coordinates found
box found
velocities found
Kinetic energy: 411492 (kJ/mol)
Assuming the number of degrees of freedom to be Natoms * 3 or Natoms * 2,
the velocities correspond to a temperature of the system
of 297.996 K or 446.995 K respectively.
Checking for atoms closer than 0.8 and not between 0.4 and 0.7,
relative to sum of Van der Waals distance:
WARNING: masses will be determined based on residue and atom names,
this can deviate from the real mass of the atom type
In case you use free energy of solvation predictions:
++++++++ PLEASE CITE THE FOLLOWING REFERENCE ++++++++
D. Eisenberg and A. D. McLachlan
Solvation energy in protein folding and binding
Nature 319 (1986) pp. 199-203
-------- -------- --- Thank You --- -------- --------
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Opening library file /usr/local/gromacs/share/top/atommass.dat
Opening library file /usr/local/gromacs/share/top/vdwradii.dat
Opening library file /usr/local/gromacs/share/top/dgsolv.dat
#Entries in atommass.dat: 82 vdwradii.dat: 26 dgsolv.dat: 7
atom# name residue r_vdw atom# name residue r_vdw distance
40 CB PRO 5 0.15 42 CD PRO 5 0.15 0.2332
50 CD1 TYR 6 0.15 58 CZ TYR 6 0.15 0.2369
52 CD2 TYR 6 0.15 58 CZ TYR 6 0.15 0.2358
78 CA PRO 9 0.15 80 CG PRO 9 0.15 0.2383
87 CB LEU 10 0.15 91 C LEU 10 0.15 0.2399
149 C VAL 16 0.15 153 CA GLN 17 0.15 0.2398
190 CG PHE 21 0.15 195 CE1 PHE 21 0.15 0.2395
191 CD1 PHE 21 0.15 193 CD2 PHE 21 0.15 0.2393
193 CD2 PHE 21 0.15 199 CZ PHE 21 0.15 0.2369
244 C VAL 26 0.15 248 CA LYSH 27 0.15 0.2371
277 CG1 VAL 30 0.15 278 CG2 VAL 30 0.15 0.2398
302 CB THR 33 0.15 306 C THR 33 0.15 0.2383
352 CG HISB 39 0.15 355 CE1 HISB 39 0.15 0.2174
354 CD2 HISB 39 0.15 355 CE1 HISB 39 0.15 0.2169
361 CA PRO 40 0.15 364 CD PRO 40 0.15 0.2395
362 CB PRO 40 0.15 364 CD PRO 40 0.15 0.2387
383 C LEU 42 0.15 387 CA ASN 43 0.15 0.2391
440 CG PHE 50 0.15 447 CE2 PHE 50 0.15 0.2371
441 CD1 PHE 50 0.15 449 CZ PHE 50 0.15 0.2331
443 CD2 PHE 50 0.15 449 CZ PHE 50 0.15 0.2371
459 C VAL 51 0.15 463 CA ALA 52 0.15 0.2376
492 CG TYR 56 0.15 497 CE1 TYR 56 0.15 0.2334
492 CG TYR 56 0.15 499 CE2 TYR 56 0.15 0.2398
497 CE1 TYR 56 0.15 499 CE2 TYR 56 0.15 0.2375
558 CA HISA 63 0.15 560 CG HISA 63 0.15 0.2398
560 CG HISA 63 0.15 564 CE1 HISA 63 0.15 0.212
563 CD2 HISA 63 0.15 564 CE1 HISA 63 0.15 0.2126
586 CG HISB 66 0.15 589 CE1 HISB 66 0.15 0.2163
588 CD2 HISB 66 0.15 589 CE1 HISB 66 0.15 0.2109
692 C GLY 79 0.15 696 CA VAL 80 0.15 0.2391
698 CG1 VAL 80 0.15 699 CG2 VAL 80 0.15 0.2384
732 CB PRO 85 0.15 734 CD PRO 85 0.15 0.2341
751 C VAL 87 0.15 755 CA SER 88 0.15 0.2397
775 CD1 TYR 90 0.15 783 CZ TYR 90 0.15 0.2391
777 CD2 TYR 90 0.15 783 CZ TYR 90 0.15 0.2398
817 CA VAL 94 0.15 819 CG1 VAL 94 0.15 0.2397
890 CD1 TYR 103 0.15 892 CD2 TYR 103 0.15 0.2384
894 CE1 TYR 103 0.15 896 CE2 TYR 103 0.15 0.2346
929 CG1 VAL 107 0.15 930 CG2 VAL 107 0.15 0.2398
969 CG TRP 112 0.15 975 CE2 TRP 112 0.15 0.2231
970 CD1 TRP 112 0.15 972 CD2 TRP 112 0.15 0.2171
970 CD1 TRP 112 0.15 975 CE2 TRP 112 0.15 0.2157
975 CE2 TRP 112 0.15 976 CE3 TRP 112 0.15 0.2367
978 CZ2 TRP 112 0.15 980 CZ3 TRP 112 0.15 0.2378
1079 C MET 123 0.15 1083 CA SER 124 0.15 0.2396
1094 CD1 LEU 125 0.15 1095 CD2 LEU 125 0.15 0.239
1216 C ASN 140 0.15 1220 CA ALA 141 0.15 0.2389
1228 CG TYR 142 0.15 1233 CE1 TYR 142 0.15 0.2379
1229 CD1 TYR 142 0.15 1231 CD2 TYR 142 0.15 0.2377
1233 CE1 TYR 142 0.15 1235 CE2 TYR 142 0.15 0.2356
1251 CB ARG 144 0.15 1263 C ARG 144 0.15 0.2347
1347 C GLY 156 0.15 1351 CA ASN 157 0.15 0.2398
1428 CG TYR 166 0.15 1433 CE1 TYR 166 0.15 0.238
1428 CG TYR 166 0.15 1435 CE2 TYR 166 0.15 0.2363
1443 CA PRO 167 0.15 1446 CD PRO 167 0.15 0.2391
1473 CD1 TYR 170 0.15 1475 CD2 TYR 170 0.15 0.237
1473 CD1 TYR 170 0.15 1481 CZ TYR 170 0.15 0.2383
1477 CE1 TYR 170 0.15 1479 CE2 TYR 170 0.15 0.2392
1530 CG1 VAL 176 0.15 1531 CG2 VAL 176 0.15 0.2373
1635 CG PHE 188 0.15 1640 CE1 PHE 188 0.15 0.2336
1635 CG PHE 188 0.15 1642 CE2 PHE 188 0.15 0.2393
1640 CE1 PHE 188 0.15 1642 CE2 PHE 188 0.15 0.2399
1686 CB GLU 194 0.15 1691 C GLU 194 0.15 0.2396
1698 CD1 LEU 195 0.15 1699 CD2 LEU 195 0.15 0.2293
1736 CA PRO 200 0.15 1738 CG PRO 200 0.15 0.2346
1762 CG1 VAL 204 0.15 1763 CG2 VAL 204 0.15 0.2344
1771 CD1 TYR 205 0.15 1773 CD2 TYR 205 0.15 0.2366
1775 CE1 TYR 205 0.15 1777 CE2 TYR 205 0.15 0.2391
1806 CD1 TYR 208 0.15 1808 CD2 TYR 208 0.15 0.2383
1810 CE1 TYR 208 0.15 1812 CE2 TYR 208 0.15 0.2356
1859 CG TYR 213 0.15 1864 CE1 TYR 213 0.15 0.2375
1860 CD1 TYR 213 0.15 1862 CD2 TYR 213 0.15 0.24
1862 CD2 TYR 213 0.15 1868 CZ TYR 213 0.15 0.2396
1864 CE1 TYR 213 0.15 1866 CE2 TYR 213 0.15 0.2366
1954 CA PRO 224 0.15 1957 CD PRO 224 0.15 0.2351
1964 CG HISA 225 0.15 1968 CE1 HISA 225 0.15 0.2137
1967 CD2 HISA 225 0.15 1968 CE1 HISA 225 0.15 0.2127
2012 CB LEU 232 0.15 2014 CD1 LEU 232 0.15 0.2396
2032 CD1 LEU 234 0.15 2033 CD2 LEU 234 0.15 0.2395
2063 CD2 HISB 237 0.15 2064 CE1 HISB 237 0.15 0.2173
2070 CA PRO 238 0.15 2072 CG PRO 238 0.15 0.2387
2236 CG TYR 255 0.15 2243 CE2 TYR 255 0.15 0.2388
2241 CE1 TYR 255 0.15 2243 CE2 TYR 255 0.15 0.237
2284 CG PHE 260 0.15 2289 CE1 PHE 260 0.15 0.2363
2285 CD1 PHE 260 0.15 2287 CD2 PHE 260 0.15 0.2389
2287 CD2 PHE 260 0.15 2293 CZ PHE 260 0.15 0.2339
2301 CG TYR 261 0.15 2308 CE2 TYR 261 0.15 0.2389
2302 CD1 TYR 261 0.15 2310 CZ TYR 261 0.15 0.2358
2304 CD2 TYR 261 0.15 2310 CZ TYR 261 0.15 0.2395
2319 CG TYR 262 0.15 2326 CE2 TYR 262 0.15 0.2376
2324 CE1 TYR 262 0.15 2326 CE2 TYR 262 0.15 0.238
Atoms outside box ( 10.4513 10.4513 10.4513 ):
(These may occur often and are normally not a problem)
atom# name residue r_vdw coordinate
2488 OW SOL 293 0.105 -0.034 2.79 4.15
2491 OW SOL 294 0.105 -0.031 5.54 9.37
2494 OW SOL 295 0.105 -0.024 3.92 10.1
2497 OW SOL 296 0.105 -0.02 5.24 10.3
2500 OW SOL 297 0.105 -0.018 4.16 8.09
2501 HW1 SOL 297 0.04 -0.027 4.18 8.19
2503 OW SOL 298 0.105 -0.018 6.61 5.17
2506 OW SOL 299 0.105 -0.016 1.37 7.5
2509 OW SOL 300 0.105 -0.015 2.23 9.93
2511 HW2 SOL 300 0.04 -0.048 2.29 10
(maybe more)-bash-2.05b$ g_rms -f 1scn_bx_w_fullMD_mv.trr -s
1scn_bx_w_CL_TPR4fullMD.tpr -o
:-) G R O M A C S (-:
Grunge ROck MAChoS
:-) VERSION 3.2.1 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2004, The GROMACS development team,
check out http://www.gromacs.org for more information.
This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.
:-) g_rms (-:
Option Filename Type Description
------------------------------------------------------------
-s 1scn_bx_w_CL_TPR4fullMD.tpr Input Structure+mass(db): tpr tpb
tpa gro g96 pdb xml
-f 1scn_bx_w_fullMD_mv.trr Input Generic trajectory: xtc trr trj
gro g96 pdb
-f2 traj.xtc Input, Opt. Generic trajectory: xtc trr trj gro g96 pdb
-n index.ndx Input, Opt. Index file
-o rmsd.xvg Output xvgr/xmgr file
-mir rmsdmir.xvg Output, Opt. xvgr/xmgr file
-a avgrp.xvg Output, Opt. xvgr/xmgr file
-dist rmsd-dist.xvg Output, Opt. xvgr/xmgr file
-m rmsd.xpm Output, Opt. X PixMap compatible matrix file
-bin rmsd.dat Output, Opt. Generic data file
-bm bond.xpm Output, Opt. X PixMap compatible matrix file
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 19 Set the nicelevel
-b time -1 First frame (ps) to read from trajectory
-e time -1 Last frame (ps) to read from trajectory
-dt time -1 Only use frame when t MOD dt = first time (ps)
-tu enum ps Time unit: ps, fs, ns, us, ms, s, m or h
-[no]w bool no View output xvg, xpm, eps and pdb files
-what enum rmsd Structural difference measure: rmsd, rho or rhosc
-[no]pbc bool yes PBC check
-fit enum rot+trans Fit to reference structure: rot+trans,
translation or none
-prev int 0 Compare with previous frame
-[no]split bool no Split graph where time is zero
-skip int 1 Only write every nr-th frame to matrix
-skip2 int 1 Only write every nr-th frame to matrix
-max real -1 Maximum level in comparison matrix
-min real -1 Minimum level in comparison matrix
-bmax real -1 Maximum level in bond angle matrix
-bmin real -1 Minimum level in bond angle matrix
-nlevels int 80 Number of levels in the matrices
Reading file 1scn_bx_w_CL_TPR4fullMD.tpr, VERSION 3.2.1 (single precision)
Reading file 1scn_bx_w_CL_TPR4fullMD.tpr, VERSION 3.2.1 (single precision)
Select group for least squares fit
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Group 0 ( System) has 110719 elements
Group 1 ( Protein) has 2433 elements
Group 2 ( Protein-H) has 1920 elements
Group 3 ( C-alpha) has 274 elements
Group 4 ( Backbone) has 822 elements
Group 5 ( MainChain) has 1097 elements
Group 6 (MainChain+Cb) has 1336 elements
Group 7 ( MainChain+H) has 1364 elements
Group 8 ( SideChain) has 1069 elements
Group 9 ( SideChain-H) has 823 elements
Group 10 ( Prot-Masses) has 2433 elements
Group 11 ( Non-Protein) has 108286 elements
Group 12 ( CL) has 4 elements
Group 13 ( HOH) has 423 elements
Group 14 ( SOL) has 107856 elements
Group 15 ( CA) has 2 elements
Group 16 ( NA) has 1 elements
Group 17 ( Other) has 108286 elements
Select a group: 1
Selected 1: 'Protein'
How many groups do you want to compare ? 1
OK. I will compare 1 group
Select group for RMSD calculation
Opening library file /usr/local/gromacs/share/top/aminoacids.dat
Group 0 ( System) has 110719 elements
Group 1 ( Protein) has 2433 elements
Group 2 ( Protein-H) has 1920 elements
Group 3 ( C-alpha) has 274 elements
Group 4 ( Backbone) has 822 elements
Group 5 ( MainChain) has 1097 elements
Group 6 (MainChain+Cb) has 1336 elements
Group 7 ( MainChain+H) has 1364 elements
Group 8 ( SideChain) has 1069 elements
Group 9 ( SideChain-H) has 823 elements
Group 10 ( Prot-Masses) has 2433 elements
Group 11 ( Non-Protein) has 108286 elements
Group 12 ( CL) has 4 elements
Group 13 ( HOH) has 423 elements
Group 14 ( SOL) has 107856 elements
Group 15 ( CA) has 2 elements
Group 16 ( NA) has 1 elements
Group 17 ( Other) has 108286 elements
Select a group: 1
Selected 1: 'Protein'
trn version: GMX_trn_file (single precision)
Reading frame 0 time 0.000 Fatal error: Error: Too many iterations
in routine JACOBI
How I could resolve the problem???
then I try g_rms:
On Friday 20 May 2005 10:42 am, Anthony Cruz wrote:
> How I could do that??? a new tpr??
>
> On Friday 20 May 2005 7:53 am, Xavier Periole wrote:
> > Anthony Cruz wrote:
> > >Hi:
> > >I run a MD of a protein in water. when I try to analyse the trajectory
> > > with g_rms the program stop by the following error :
> > >Fatal error: Error: Too many iterations in routine JACOBI
> > >What could be the cause? How I can resolve the problem???
> >
> > That is certainly due to a mismatch between your reference topology and
> > the content of
> > the trajectory ... make an topology that fits the trajectory.
>
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