[gmx-users] error when running grompp

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 27 02:59:33 CEST 2011

On 4/27/2011 6:21 AM, delara aghaie wrote:
> Dear Gromacs users
> I ahve a dppc monolayer on water layer 9tip4p-2005). I have added 8 Mg 
> and 16 Cl ions using genion and now want to use grompp and then start 
> the simulation to see the effect of ions on the pressure-area isotherm 
> of the system.
> running grompp in gromacs 3.3 I see he following error:

Unless you have an important reason of continuity for using GROMACS 3.3, 
you will get much better performance from the latest GROMACS version.


> please help em to solve it.let me knoe please what is cpp?
> Thanks in advance
> D. Aghaie
> -bash-3.2$ grompp_mpi -c dppc-salt-Mg-0.1.gro -f run.mdp -n 
> indexsalt-Mg.ndx -p topoldppc.top -o topol.tpr -np 8
> :-)  G  R  O  M  A  C  S  (-:
>                    Groningen Machine for Chemical Simulation
>                              :-)  VERSION 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) 2001-2004, The GROMACS development team,
>             check out http://www.gromacs.orgfor 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_mpi  (-:
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f        run.mdp  Input, Opt!  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c dppc-salt-Mg-0.1.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 indexsalt-Mg.ndx  Input, Opt!  Index file
> -deshuf  deshuf.ndx  Output, Opt. Index file
>   -p  topoldppc.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o      topol.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      8  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 8 nodes...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> calling cpp...
> topoldppc.top:7:20: error: ions.itp: No such file or directory
> cpp exit code: 256
> Tried to execute: 'cpp  -I/apps/gromacs/3.3/share/top  topoldppc.top > 
> gromppzVWhWp'
> The 'cpp' command is defined in the .mdp file
> processing topology...
> Generated 1369 of the 2211 non-bonded parameter combinations
> Excluding 3 bonded neighbours for DPP 64
> turning all bonds into constraints...
> Excluding 2 bonded neighbours for SOL 4152
> turning all bonds into constraints...
> Cleaning up temporary file gromppzVWhWp
> -------------------------------------------------------
> Program grompp_mpi, VERSION 3.3
> Source code file: toppush.c, line: 1264
> Fatal error:
> No such moleculetype Mg
> -------------------------------------------------------
> Thanx for Using GROMACS - Have a Nice Day

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