[AMBER] Using the RED Server Dev. to parameterize a model transition state

From: Kamali Sripathi <ksripath.umich.edu>
Date: Fri, 6 Dec 2013 16:19:46 -0500

Dear AMBER Users,

I am using the RED Server Development to parameterize a model compound for
the transition state and different protonation states of one or both of the
nonbridging oxygens in ribozyme cleavage. My questions are regarding a
portion of the Project.config file that one may optionally include to
override default options (
There is a portion of the Project.config file that deals with
intramolecular constraints (INTRA-MCC). My questions are:

   - How does one decide what value to assign for intramolecular
   - How does one decide whether or not to keep the intra-molecular charge
   constraints through the second stage of fitting (i.e., INTRA-MCC1 vs.

If my questions are trivial ones, please direct me to the appropriate
Thank you all very much, and have a great day,

Kamali Sripathi
AMBER mailing list
Received on Fri Dec 06 2013 - 13:30:02 PST
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