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 (
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Project.config).
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
constraints?
- 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.
INTRA-MCC2)?
If my questions are trivial ones, please direct me to the appropriate
references.
Thank you all very much, and have a great day,
Kamali Sripathi
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Received on Fri Dec 06 2013 - 13:30:02 PST
