AMBER Archive (2006)

Subject: AMBER: A dummy atom on the center of solute molecule

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Mon May 22 2006 - 06:49:23 CDT

Dear all.

 

Hi.

I want to do umbrella sampling MD along the reaction coordinate between
protein and

the center of ligand molecule.

So I need to set a dummy atom on the center of ligand molecule.

How should I put a dummy atom in pdb file in Amber8?

 

Could you please give me any suggestions?

Thank you.

 

Acci Okabe

 

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