[gmx-users] Invalid atom number 6415 in indexfile
Liu Shiyong
liushiyong at gmail.com
Wed Jan 21 20:36:02 CET 2009
Hi,
I got an error when do grompp: The input PDB file comes from the output
of GROMACS by trajconv command.
*Here is the log from grompp:*
Option Filename Type Description
------------------------------------------------------------
-f em.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c r-l_103703_G53a6.minim_traj_withH_0.6.gro Input Generic
structure: gro g96 pdb tpr tpb tpa xml
-r conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-rb conf.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa
xml
-n r-l_103703_G53a6.minim_traj_withH_0.6.ndx Input, Opt! Index file
-deshuf deshuf.ndx Output, Opt. Index file
-p r-l_103703_G53a6.minim_traj_withH_0.6.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o r-l_103703_G53a6.minim_traj_withH_0.6.input.tpr Output Generic
run input: tpr tpb tpa xml
-t traj.trr Input, Opt. Full precision trajectory: trr trj
-e ener.edr Input, Opt. Generic energy: edr ene
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 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-np int 1 Generate statusfile for # nodes
-[no]shuffle bool no Shuffle molecules over nodes
-[no]sort bool no Sort molecules according to X coordinate
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-load string Releative load capacity of each node on a
parallel machine. Be sure to use quotes around
the string, which should contain a number for
each node
-maxwarn int 10 Number of warnings after which input processing
stops
-[no]check14 bool no Remove 1-4 interactions without Van der Waals
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
Generated 165 of the 1596 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein_A 1
Excluding 3 bonded neighbours for Protein_B 1
Excluding 3 bonded neighbours for Protein_D 1
Excluding 3 bonded neighbours for Protein_E 1
NOTE:
System has non-zero total charge: -4.000003e+00
processing coordinates...
double-checking input for internal consistency...
WARNING 1 [file "r-l_103703_G53a6.minim_traj_withH_0.6.top", line 41]:
With nstlist=0 atoms are only put into the box at step 0, therefore
drifting atoms might cause the simulation to crash.
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 6415 elements
Making dummy/rest group for Acceleration containing 6415 elements
Making dummy/rest group for Freeze containing 6415 elements
-------------------------------------------------------
Program grompp, VERSION 3.3.3
Source code file: ../../../../src/kernel/readir.c, line: 838
*Fatal error:
Invalid atom number 6415 in indexfile*
-------------------------------------------------------
"Bailed Out Of Edge Synchronization After 10,000 Iterations" (X/Motif)
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, 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.
:-) grompp (-:
creating statusfile for 1 node...
calling /usr/bin/cpp...
processing topology...
# G96BONDS: 6557
# G96ANGLES: 9621
# PDIHS: 3328
# IDIHS: 3469
# LJ14: 10148
*Here is the log from make_ndx:*
:-) G R O M A C S (-:
Gnomes, ROck Monsters And Chili Sauce
:-) VERSION 3.3.3 (-:
Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, 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.
:-) make_ndx (-:
Option Filename Type Description
------------------------------------------------------------
-f r-l_103703_G53a6.minim_traj_withH.pdb Input, Opt! Generic structure:
gro g96 pdb tpr tpb tpa xml
-n index.ndx Input, Opt., Mult. Index file
-o r-l_103703_G53a6.minim_traj_withH_0.6.ndx Output Index 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 0 Set the nicelevel
-natoms int 0 set number of atoms (default: read from
coordinate or index file)
Reading structure file
Opening library file /usr/share/gromacs/top/aminoacids.dat
gcq#137: "Shit Happens" (Pulp Fiction)
Going to read 0 old index file(s)
Analysing residue names:
There are: 0 OTHER residues
There are: 603 PROTEIN residues
There are: 0 DNA residues
Analysing Protein...
0 System : 6416 atoms
1 Protein : 6416 atoms
2 Protein-H : 4898 atoms
3 C-alpha : 603 atoms
4 Backbone : 1809 atoms
5 MainChain : 2416 atoms
6 MainChain+Cb : 2982 atoms
7 MainChain+H : 2997 atoms
8 SideChain : 3419 atoms
9 SideChain-H : 2482 atoms
nr : group ! 'name' nr name 'splitch' nr Enter: list groups
'a': atom & 'del' nr 'splitres' nr 'l': list residues
't': atom type | 'keep' nr 'splitat' nr 'h': help
'r': residue 'res' nr 'chain' char
"name": group 'case': case sensitive 'q': save and quit
>
Removed group 1 'Protein'
Removed group 2 'Protein-H'
Removed group 3 'C-alpha'
Removed group 4 'Backbone'
Removed group 5 'MainChain'
Removed group 6 'MainChain+Cb'
Removed group 7 'MainChain+H'
Removed group 8 'SideChain'
Removed group 9 'SideChain-H'
>
Found 2378 atoms with chain identifiers D AND E
1 chDANDE : 2378 atoms
>
Found 4038 atoms with chain identifiers A AND B
2 chAANDB : 4038 atoms
>
--
Shiyong Liu
Postdoc
center for bioinformatics in the university of kansas
Lab: (785)864-1962
Email: syliu at ku.edu (shiyongliu at ku.edu or liushiyong at ku.edu)
Homepage: http://www.people.ku.edu/~syliu
Lab: http://vakser.bioinformatics.ku.edu/people
Phone: (785) 864-1962
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