[gmx-users] covalent bond between ligand and protein

David van der Spoel spoel at xray.bmc.uu.se
Tue Jan 13 09:27:00 CET 2004

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 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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