[gmx-users] Charmm27 parameterization problems in GMX 4.5.1

[Christian Seifert]

Thx Roland,

with the help of -pp and -debug we found out, that we included the new
parameters in the wrong way. First bonded, and then nonbonded. It should
be the other way around.

Greets,
Christian

On Fri, 2010-10-08 at 11:09 -0400, Roland Schulz wrote:
> 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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> 
> 
> -- 
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
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-- 
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