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