[gmx-users] Error running grompp

[Florian Haberl]

Hi,

On Friday, 6. July 2007 08:03, fufengliu at tju.edu.cn wrote:
> Dear gmx users:
>         I m carrying a protein explicit solvent simulation  using gromacs 
> 3.3, then i added water, but in next step, I m getting the following error,

check your top and gro file, something seriously is wrong, perhaps you have 
added wrong forcefield in your top file.

>
>  grompp -f em.mdp -c try.gro -p A.top -o A_em.tpr
>
>                          :-)  G  R  O  M  A  C  S  (-:
>
>         Getting the Right Output Means no Artefacts in Calculating Stuff
>
>                             :-)  VERSION 3.3.1  (-:
>
>       Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
>        Copyright (c) 1991-2000, University of Groningen, The Netherlands.
>              Copyright (c) 2001-2006, 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  (-:
>
> 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        try.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      index.ndx  Input, Opt.  Index file
> -deshuf  deshuf.ndx  Output, Opt. Index file
>   -p          A.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o       A_em.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]renum   bool    yes  Renumber atomtypes and minimize number of
>                             atomtypes
>
> creating statusfile for 1 node...
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 1284 of the 1485 non-bonded parameter combinations
> Cleaning up temporary file grompp3wF5if
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: toputil.c, line: 61
>
> Fatal error:
> Atomtype 'C3' not found!
> -------------------------------------------------------
>
> "Baby, It Aint Over Till It's Over" (Lenny Kravitz)
> Can you tell me how to correct it?
> Best Regards!
> Fufeng liu
>
>
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Greetings,

Florian

-- 
-------------------------------------------------------------------------------
 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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