[gmx-users] Ligand bond

[abelius]

Hi Tsjerk, Andrea

Thx for your answers.
So if I understand correctly adding the bond to specbond.dat isn't 
necessary ?
Btw, do you know if someone already made a perl-module for gromacs?

Greetings,
Abel

Tsjerk Wassenaar wrote:

> 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 
> <mailto: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 <mailto:abelius at gmail.com>>
>     To: "Discussion list for GROMACS users" < gmx-users at gromacs.org
>     <mailto: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> <mailto: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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