[gmx-users] Fatal error with grompp(with detail process)

[Justin A. Lemkul]

Jenny Hsu 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

We just had a discussion about this:

http://www.gromacs.org/pipermail/gmx-users/2008-November/038282.html

You can copy the relevant portions of lipid.itp into the appropriate sections in 
ffG53a6nb.itp/ffG53a6bon.itp.  Otherwise, including the files as you have will 
not work.

-Justin

>  
> *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 <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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================