[gmx-users] covalent bond between ligand and protein

[David van der Spoel]

On Tue, 2004-01-13 at 17:09, muthu12 at cox.net wrote:
> Is there any example for specbond.dat How grommp will read that file
> thank you
share/top/specbond.dat

it's read by pdb2gmx

> prabhakaran
> > 
> > From: David van der Spoel <spoel at xray.bmc.uu.se>
> > Date: 2004/01/13 Tue AM 03:17:02 EST
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] covalent bond between ligand and protein
> > 
> > On Mon, 2004-01-12 at 23:17, muthu12 at cox.net wrote:
> > > I have difficulty to make a bond netween protein and the ligand. I get out of bounds error message. Even the constraints wont' work. Is it any way other making the ligand as a part of
> > > protein
> > 
> > there is a way. you have to make an rtp entry for your ligand, and you
> > have to define a special bond (specbond.dat). It maybe that you have to
> > update your *bon.itp files to add bonded parameters between your ligand
> > and protein.
> > 
> > > thank you
> > > Prabhakara
> > > 
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the 
> > > www interface or send it to gmx-users-request at gromacs.org.
> > -- 
> > David.
> > ________________________________________________________________________
> > David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
> > Dept. of Cell and Molecular Biology, Uppsala University.
> > Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> > phone:	46 18 471 4205		fax: 46 18 511 755
> > spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++