[gmx-users] grompp problem

Ran Friedman r.friedman at bioc.unizh.ch
Thu Mar 15 13:37:59 CET 2007

Dir Tom,

I have a version of ffG53a6.rtp with PTR. It worked for me in
simulations, though I never rigorously checked the FF parameters, so no
Contact me off list if you're interested.


Tom Lenaerts wrote:
> Hi all,
> To work with PTR in gromacs I added the residue information in
> ffG53a6.rtp, added the unknown atom names () to  ffG53a6.atp and added
> the residue name to aminoacids.dat.
> this allowed me to make the topology file  using pdb2gmx, create the 
> box and fill it with water.  Now I want to perform the
> energy minimisation by first doing grompp.  Then
> I get an error
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 165 of the 1596 non-bonded parameter combinations
> Cleaning up temporary file grompp8BMpzT
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toputil.c, line: 61
> Fatal error:
> Atomtype 'CB' not found!
> -------------------------------------------------------
> Yet I added the atom CB to the ffG53a6.atp file ... so what can be the
> problem here?
> Tom
> ------------------------------------------------------------------------
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Ran Friedman
Postdoctoral Fellow
Computational Structural Biology Group (A. Caflisch)
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
CH-8057 Zurich, Switzerland
Tel. +41-44-6355593
Email: r.friedman at bioc.unizh.ch
Skype: ran.friedman

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