AMBER Archive (2006)

Subject: AMBER: distance restraints for umbrella sampling

From: mkseo (seo_at_ualberta.ca)
Date: Thu Apr 27 2006 - 17:21:16 CDT

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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