[gmx-users] Charmm27 parameterization problems in GMX 4.5.1

Christian Seifert cseifert at bph.ruhr-uni-bochum.de
Fri Oct 8 11:48:11 CEST 2010

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


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
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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