[AMBER] Putting oxygen molecules around protein structure

From: Shukla, Saurabh <sshukla4.illinois.edu>
Date: Thu, 12 Mar 2015 03:38:24 +0000

Dear all,
I am trying to study a diffusion process inside a protein. I want to put 500 oxygen molecules outside the protein and want to simulate the system to see the trajectory of oxygen molecules in the protein cavities.

Please suggest how I can go about putting oxygen molecules in the solvent. Is there any direct command to replace some of the water molecules by oxygen molecules? If not, which files would I need to change in order to introduce oxygen molecules in system?

Thank You.

Saurabh Shukla,
Graduate Research Assistant,
Department of Chemical and Biomolecular Engineering,
University of Illinois at Urbana Champaign, IL

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Received on Wed Mar 11 2015 - 21:00:02 PDT
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