[gmx-users] grompp problem

[Olivier Perin]

Hi Tom,

setting rtp and atp files is not sufficient in order to make a complete 
topology in GMX. You have to added also some new bonds, angles, 
dihidrals etc... in ff*bon.itp ff*nb.itp. Check all of this. Look at all 
the files for one force field (ffG53a6.* in the top folder). They may 
contain information that you have maybe missed.

But your problem may comes from elsewhere.....

Good luck


> 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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-- 
------------------------------------
Olivier PERIN - Institut Pasteur
Unite de Bioinformatique Structurale
25-28, rue du Dr Roux 75724 Paris Cedex 15
Tel: +331 40 61 38 84
Fax: +331 45 68 87 19
mail: operin at pasteur.fr
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