[gmx-users] em fatal error!

[lina]

On Mon, Apr 2, 2012 at 5:27 PM, ankita oindrila <oinanki at gmail.com> wrote:
> We are trying to do simulation of lysozyme in water.
>
> step with problem : energy minimization.
>
> command given: [root at localhost gromacs-4.0.5]# grompp -f minim.mdp -c
> 1AKI_solv_ions.gro -p topol.top -o em.tpr
>
>                          :-)  G  R  O  M  A  C  S  (-:
>
>         Getting the Right Output Means no Artefacts in Calculating Stuff
>
>                             :-)  VERSION 4.0.5  (-:
>
>
>       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  (-:
>
> Option     Filename  Type         Description
> ------------------------------------------------------------
>   -f      minim.mdp  Input, Opt!  grompp input file with MD parameters
>  -po      mdout.mdp  Output       grompp input file with MD parameters
>   -c 1AKI_solv_ions.gro  Input        Structure file: gro g96 pdb tpr tpb
> tpa
>   -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>  -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
>   -n      index.ndx  Input, Opt.  Index file
>   -p      topol.top  Input        Topology file
>  -pp  processed.top  Output, Opt. Topology file
>   -o         em.tpr  Output       Run input file: tpr tpb tpa
>   -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
>   -e       ener.edr  Input, Opt.  Energy file: edr ene
>
> Option       Type   Value   Description
> ------------------------------------------------------
> -[no]h       bool   no      Print help info and quit
> -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.
> -[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
>                             sites
> -maxwarn     int    0       Number of allowed warnings during input
> processing
> -[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...
> processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaa.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaanb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffoplsaabon.itp
> Generated 332520 of the 332520 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 332520 of the 332520 1-4 parameter combinations
> Opening library file /usr/local/gromacs/share/gromacs/top/spce.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.5

You use Version 4.0.5.

If I remember correctly, the earlier version has different pname.
(seems one is NA+, one is NA)

If I were you, I would update to latest version and try.

> Source code file: toppush.c, line: 1641
>
> Fatal error:
> No such moleculetype NA
>
> what should we do????
>
>
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