AMBER Archive (2006)

Subject: Re: AMBER: FIX conformation of a ligand

From: David A. Case (case_at_scripps.edu)
Date: Thu Jul 06 2006 - 09:30:01 CDT

On Thu, Jul 06, 2006, a a wrote:
>
> I am trying to use AMBER to calculate a Protein-ligand structure. As I got
> crystal structure for the ligand, I want to keep it, how can I fix the
> conformation of a ligand in amber? While allows the relative position of
> the ligand to the protein flexible and able to optimize during optimization?

Amber has no direct facilities for "rigid body" dynamics. In some cases, you
could add internal restraints (similar to NMR restraints) to keep the ligand
conformation nearly fixed. But in truth, Amber was not designed for the sort
of calculation you have in mind.

...regards...dac

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