[gmx-users] Fatal error with grompp(with detail process)
Jenny Hsu
jenny.h1087 at gmail.com
Fri Nov 28 10:12:35 CET 2008
Hi Tsjerk:
One of my friends combines popc information into G53a6
that's why i try to use G53a6.
If its not working, which force field should i choose?
Best regards,
Jenny
2008/11/28 Tsjerk Wassenaar <tsjerkw at gmail.com>
> Hi Jenny,
>
> The files lipid.itp/popc.itp contain references to atom types which
> are not in the G53a6 force field; that combination just doesn't work.
> lipid.itp/popc.itp were written to be used with another force field.
> It's generally not a good idea to mix force fields.
>
> Cheers,
>
> Tsjerk
>
> On Fri, Nov 28, 2008 at 8:58 AM, Jenny Hsu <jenny.h1087 at gmail.com> wrote:
> > Hi all:
> > I have a problem with grompp
> > I want to making "POPC+protein" file
> > and I search the archieve and follow the process
> > 1.run pdb2gmx for protein only
> > 2.add below parameters into my topology file
> > #include "ffG53a6.itp"
> > #include "lipid.itp"
> > #include "popc.itp"
> > 3.adjust the [ molecules ] section to list the number and type of my
> > components
> > 4.run editconf and genbox
> > 5.run grompp and it shows
> > Fatal error:
> > Atomtype CA not found
> >
> > Below is all information it shows
> > Can someone help me to solve this problem?
> > I am appreciate with that.
> > Thaks.
> > :-) G R O M A C S (-:
> > Getting the Right Output Means no Artefacts in Calculating Stuff
> > :-) VERSION 4.0 (-:
> > 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 em.mdp Input, Opt! grompp input file with MD parameters
> > -po mdout.mdp Output grompp input file with MD parameters
> > -c 1UEO-nowater_water.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 1UEO-nowater.top Input Topology file
> > -pp processed.top Output, Opt. Topology file
> > -o 1UEO-nowater_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
> > Ignoring obsolete mdp entry 'title'
> > Ignoring obsolete mdp entry 'cpp'
> > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> > checking input for internal consistency...
> > processing topology...
> > Opening library file /usr/local/md/share/gromacs/top/ffG53a6.itp
> > Opening library file /usr/local/md/share/gromacs/top/ffG53a6nb.itp
> > Opening library file /usr/local/md/share/gromacs/top/ffG53a6bon.itp
> > Opening library file /usr/local/md/share/gromacs/top/ff_dum.itp
> > WARNING 1 [file lipid.itp, line 14]:
> > Overriding atomtype LO
> > WARNING 2 [file lipid.itp, line 15]:
> > Overriding atomtype LOM
> > WARNING 3 [file lipid.itp, line 16]:
> > Overriding atomtype LNL
> > WARNING 4 [file lipid.itp, line 17]:
> > Overriding atomtype LC
> > WARNING 5 [file lipid.itp, line 18]:
> > Overriding atomtype LH1
> > WARNING 6 [file lipid.itp, line 19]:
> > Overriding atomtype LH2
> > WARNING 7 [file lipid.itp, line 20]:
> > Overriding atomtype LP
> > WARNING 8 [file lipid.itp, line 21]:
> > Overriding atomtype LOS
> > WARNING 9 [file lipid.itp, line 22]:
> > Overriding atomtype LP2
> > WARNING 10 [file lipid.itp, line 23]:
> > Overriding atomtype LP3
> > WARNING 11 [file lipid.itp, line 24]:
> > Overriding atomtype LC3
> > WARNING 12 [file lipid.itp, line 25]:
> > Overriding atomtype LC2
> > WARNING 13 [file lipid.itp, line 108]:
> > Overriding non-bonded parameters,
> > old: 0.00238804 3.38411e-06 new
> > LNL C 1 2.387718e-03 2.389594e-06
> > -------------------------------------------------------
> > Program grompp, VERSION 4.0
> > Source code file: toppush.c, line: 793
> > Fatal error:
> > Atomtype CA not found
> >
> >
> > --
> > Jenny Hsu, Biotechnology Dept.,
> > Ming Chuan University, Taiwan, R.O.C
> >
> > _______________________________________________
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>
>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
> _______________________________________________
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>
--
Jenny Hsu, Biotechnology Dept.,
Ming Chuan University, Taiwan, R.O.C
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