[AMBER] Freezing atoms in MCPB gaussian small_opt calculations

From: David William Kastner <kastner.mit.edu>
Date: Wed, 4 Aug 2021 19:02:39 +0000

Hi all,
During the MCPB protocol, is it valid to fix the alpha carbon atom positions in the small_opt Gaussian optimization? When I perform the geometry optimization for the small_opt model, one of the sidechains moves unnaturally and interacts with a nearby residue that it would never be able to reach. I could fix this by freezing the alpha carbon of this residue during the optimization. I was wondering if this will distort or invalidate the MCPB calculation results?

David 

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David Kastner
Ph.D. student | Bioengineering
MIT | Kulik Lab
kastner.io
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Received on Wed Aug 04 2021 - 12:30:02 PDT
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