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

From: Kamali Sripathi <>
Date: Mon, 9 Dec 2013 11:30:10 -0500

Dear Francois,

Thank you very much for your reply and all the help, and I'm sorry for my
late reply.

I have a few follow-up questions:

when you say "RED Perl" it looks like you're referring to the RED Server (, which appears to interface with the
most recent version of the RED source code, is that right?

I'm unable to access the reference you cite here: "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" I
just wanted to make sure that you were referring to the 1995 Cieplak et al
paper in Journal of Computational Chemistry?

I was also wondering if you could provide some insight on how to pick the
atoms for the MOLECULE1-ROTATE and MOLECULE1-TRANSLATE flags specified in
the Project.config file. Would it be very bad to leave these flags out in
my charge derivation?

Thank you very much, and have a great day,


On Sat, Dec 7, 2013 at 4:30 PM, FyD <> wrote:

> 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.
> > INTRA-MCC2)?
> In general you want to use the way defined by Cieplak et al. i.e.
> See
> 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 Mon Dec 09 2013 - 09:00:02 PST
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