AMBER: distance restraints for umbrella sampling

From: mkseo <seo.ualberta.ca>
Date: Thu, 27 Apr 2006 16:21:16 -0600

Hi Amber users,

I am trying to calculate potentials of mean force of protein-ligand
dissociation using umbrella sampling.

The reaction coordinates is distance between center-of-mass of protein
and center-of-mass of ligand.
How can I define the distance between center-of-mass of protein and
center-of-mass of ligand in xx.RST file?
The protein has 247 residues and ligand has 4 residues.
Do I need to group the protein and ligand separately and define their
center-of-mass?

Also, what does IAT mean in distance restraints? I already read the
manual but it is still confusing.

Can anyone help about it?

Thanks.

Mikyung


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Received on Sun Apr 30 2006 - 06:07:08 PDT
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