AMBER Archive (2009)
Subject: Re: [AMBER] Pentavalent Phosphorous and Antechamber
From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Wed Jun 03 2009 - 11:35:26 CDT
On Wed, Jun 03, 2009, Peterson, Matthew W. wrote:
> We are trying to run MD on a transition state, which contains a
> pentavalent phosphorous.
Just an (obvious?) comment: antechamber is designed to estimate force fields
for stable conformers of organic molecules. It's not going to work (for
reasons beyond the specific messages you encountered) for transition states.
You are probably going to need to create a force field by hand. You might
also consider using EVB to generate what you need.
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