[gmx-users] Charmm27 parameterization problems in GMX 4.5.1

[Roland Schulz]

Hi,

one possible reason could be that the files are not included correctly.
Check the -pp output. Otherwise it is difficult to tell without the files.

Roland

On Fri, Oct 8, 2010 at 5:48 AM, Christian Seifert <
cseifert at bph.ruhr-uni-bochum.de> wrote:

> Hi GMXers,
>
> this is a Mail from one of my colleagues (who is not yet member of
> this )
> Hi GMXers,
>
> a colleague of mine (who is not yet member of our enlightened list, but
> maybe I can convince him, if we find a solution.. ^^) has a problem
> after he had copied functioning CHARMM parameters to GMX. I tried to
> solve the problem, but my trained knowledge on parameterization of OPLS
> parameters in GMX 4.0 was obviously not sufficient for CHARMM and GMX
> 4.5.
>
> Greets,
> Christian
>
>
> Dear Users,
>
> After using the
>
> grompp -v -f minim.mdp -c hpgk_open_adp_bpg-water.gro -p
> hpgk_open_adp_bpg.top -o hpgk_open_adp_bpg-water.tpr
>
> Gromacs command, I got the following error message from grompp
>
> Program grompp, VERSION 4.5.1
>
> Source code file: ../../../gromacs-4.5.1/src/kernel/toppush.c, line: 631
>
> Fatal error:
>
> Unknown bond_atomtype CN7
>
> I have a system of a protein in complex with two substrates: ADP and
> BIPG (bis-phosphoglycerate). I am using the CHARMM27 force field. I have
> added new parameters for BIPG in the corresponding .itp files (bonded
> paramerers to ffnabonded.itp and non-bonded parameters to
> ffnanonbonded.itp). All the atomtypes of BIPG are defined in
> atomtypes.atp. I have built the topology for BIPG in .rtp file and
> hyrodgen data base file .hdb as well. Moreover I have added BIPG as new
> residue in the residuetypes.dat file. I have created succesfully a .top
> file for my system and molecule.itp files for the protein and each
> substrates by pdb2gmx. The .top and molecule.itp files are in accordance
> with the rtp files. However grompp cannot recognize the bond parameter
> for the CN7 atom of BIPG. Is there any idea to solve this problem?
>
>
> Thank you in advance,
>
> Zoltan Palmai
>
> --
> M.Sc. Christian Seifert
> Department of Biophysics
> University of Bochum
> ND 04/67
> 44780 Bochum
> Germany
> Tel: +49 (0)234 32 28363
> Fax: +49 (0)234 32 14626
> E-Mail: cseifert at bph.rub.de
> Web: http://www.bph.rub.de
>
> --
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