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

From: FyD <>
Date: Sat, 07 Dec 2013 22:30:00 +0100

Dear Kamali,

> 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.

Classical geometry optimization as implemented in R.E.D. will likely
generate a true minimum; not a TS.

So better first characterizing the TS & loading the corresponding QM
log file as input by setting OPT_Calc = "Off" & MEPCHR_Calc = "On" in
the file

> 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:

INTRA-MCC in R.E.D. Perl = INTRA-MCC1 in R.E.D. Python, which is the
classical way to set up intra-molecular charge constraint...
See Cieplak et al. in

> - How does one decide what value to assign for intramolecular
> constraints?

In general when one wants to remove a part of a whole molecule to
generate a molecular fragment the intra-mcc total charge value takes
an integer value (& this integer value is very often zero).

See also a discussion about the relation between the chemical group
involved in the constraint & the total charge of this constraint:

> - 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.

In general you want to use the way defined by Cieplak et al. i.e. INTRA-MCC1

run both types of intra-mcc on the CH3CO group in a dipeptide model to
study the differences; in short an intra-mcc1 is only applied in the
1st resp input, while intra-mcc2 is applied in both resp inputs; the
later allows charge equivalencing for CH2 and/or CH3 groups when
involved in the constraint...

> If my questions are trivial ones, please direct me to the appropriate
> references.

no trivial question - do not worry ;-)

R.E.D. Python is not yet published - still coding new features...
R.E.D. Perl is published:

regards, Francois

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Received on Sat Dec 07 2013 - 14:00:02 PST
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