Re: AMBER: minimize a covalently bounded protein-ligand complex

From: David A. Case <>
Date: Thu, 30 Oct 2003 15:50:11 -0800

On Thu, Oct 30, 2003, Eric Hu wrote:

> Hi, I am trying to minize a complex that has a covalent bond between one
> lysine of the protein and the ligand ketone (in fact it is an enamine). How
> do I achieve minimization? I am thinking to build the ligand into an
> unnatural residue but need more suggestions. Thanks.

Don't be afraid to just experiment. I'd start with LYS and use the "edit"
command in xleap to draw in and bond the ligand. Then save this (saveOff
probably) as a new residue, and modify the pdb file so that the lys+ligand
coordinates appear as the new name.

...good luck...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
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Received on Thu Oct 30 2003 - 23:53:01 PST
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