[gmx-users] covalent bond between ligand and protein

[muthu12 at cox.net]

Is there any example for specbond.dat How grommp will read that file
thank you
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
> > 
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> -- 
> 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
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