[gmx-users] em fatal error!

[Erik Marklund]

2 apr 2012 kl. 16.02 skrev 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.

Upgrading may be a good thing for many reasons. To see what are the names of ions, check ions.itp.

> 
>> Source code file: toppush.c, line: 1641
>> 
>> Fatal error:
>> No such moleculetype NA
>> 
>> what should we do????
>> 
>> 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html

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