AMBER Archive (2005)

Subject: RE: AMBER: a bimolecular reaction

From: Yong Duan (duan_at_ucdavis.edu)
Date: Fri Jul 22 2005 - 14:25:09 CDT

Sorry, everybody. Did not realize it was an old question.

yong

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Yong Duan
Sent: Friday, July 22, 2005 10:44 AM
To: amber_at_scripps.edu
Subject: Re: AMBER: a bimolecular reaction

The alcohol hydrogen has a van der Waals zero van der Waals radius,
allowing it collapse to the negatively charge carboxylic acid. You
probably need to turn on SHAKE for all atoms (not limited to hydrogens).

yong

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