[gmx-users] Ligand bond

[Tsjerk Wassenaar]

Hi Abel, Andrea,

The file specbond.dat is used by pdb2gmx. If you have a topology from the
prodrg server, but need to have the ligand covalently linked to the protein,
then you have to merge the two topologies and manually add bond, angles,
dihedrals, improper dihedrals, pairs and maybe additional exclusions. There
were some posts recently on scripts for merging topologies and if I'm not
mistaken the scripts can be downloaded from the contributions section on
www.gromacs.org <http://www.gromacs.org>.

Hope it helps,

Tsjerk

On 10/19/05, Andrea Carotti <and.carotti at farmchim.uniba.it> wrote:
>
> Dear Abel,
> If I'm not wrong, you must add the bond using a file called
> specbond.dat. By default, the file used is in the gromacs path, but you
> can
> modify it and make a copy in the directory when you're working on. You
> must
> specify the atom name, the interacting residue and ligand names, and the
> distance between them. If everything goes fine, you will see during the
> preparation steps (perhaps grompp...i don't remember well) the link
> creation.
> Hope this help
> Andrea
>
> ----- Original Message -----
> From: "abelius" <abelius at gmail.com>
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Sent: Wednesday, October 19, 2005 11:38 AM
> Subject: Re: [gmx-users] Ligand bond
>
>
> > It's a covalent bond. When I look at the .gro file before EM the bond is
> > there, after EM it no longer is ...
> > Grompp Doesn't give any warnings.
> >
> >
> > David Mobley wrote:
> >
> >> The "bond"? Is it covalently bound? If not, what do you mean? Do you
> get
> >> any warnings when you run grompp?
> >>
> >> On 10/18/05, *abelius* < abelius at gmail.com <mailto:abelius at gmail.com>>
> >> wrote:
> >>
> >> Dear all,
> >>
> >> I'm trying to run a simulation of a ligand bound to an enzyme. To
> >> produce the *.itp I used the PRODRG server.
> >> All goes well a first, but when I try to do an EM the bond between
> >> enzyme and protein breaks.
> >>
> >> Does anyone knows how I can fix this ?
> >>
> >> thx in advance,
> >>
> >> Abel
> >>
> >>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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