AMBER Archive (2008)

Subject: AMBER: Ligand energy minimization

From: Dong Xu (d1xu_at_ucsd.edu)
Date: Mon May 12 2008 - 17:07:31 CDT

Hi All,

I was wondering about the procedure to set up Amber to perform energy
minimization of the ligand in the protein binding site environment.
I'd like to first treat protein rigid and only optimize the ligand. If
possible, I'd like to also try optimize both ligand and selected
binding site residues.

Any suggestions are greatly appreciated.

Dong Xu
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