From: Martin, Erik W (Erik.Martin_at_stjude.org)
Date: Tue Nov 20 2012 - 08:14:11 CST
Its hard to say without seeing some specifics like how much the "bent" and "extended" structures actually vary. However, I'd be inclined to say no, you shouldn't do this. Even if in a vacuum the energy minimized state of the cofactor is extended this does not mean it will remain that way in a protein environment. The CS coordinates might be perfectly accurate. My suggestion would be to rerun the Gaussian calculation. This time, fix heavy atoms that are well resolved in the CS and let the rest of the cofactor minimize.
From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] On Behalf Of Dhiraj Srivastava [dhirajks_at_gmail.com]
Sent: Tuesday, November 20, 2012 7:26 AM
Subject: namd-l: Parametarization and geometry optimization. .
I am trying to develop Charmm parameter for my cofactor. While doing geometry optimization by Gaussian, the Cofactor is going from the bend conformation (from Crystal structure) to extended conformation. Now my question is, the cofactor in my protein is in bend conformation and the parameter I am developing is for extanded conformation, So is it ok to use the parameter for extended conformation into my simulation?
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