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

From: FyD <>
Date: Mon, 09 Dec 2013 20:56:21 +0100

Dear Kamali,

> 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?

R.E.D. Perl means R.E.D. III.x at
and R.E.D. IV at

the last version is R.E.D. Python at

> 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?


P. Cieplak, W.D. Cornell, C. Bayly & P.A. Kollman, Application of the
multimolecule and multiconformational RESP methodology to biopolymers:
Charge derivation for DNA, RNA, and proteins. J. Comput. Chem. 1995,
16, 1357-1377,

Do you need the pdf file?

> 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?

- TRANSLATE will show you that translating has to effect on the MEP
grid points.
- ROTATE means only rotations
- REORIENT means rotation & translation (rigid body reorientation).
ROTATE/REORIENT will have the same effect on the MEP grid points.

just remove the corresponding keywords from the Project.config file
and let the default do the job; REORIENT is automatically selected
using a pair(s) of three non-linear atoms X Y Z; and then Z Y X.

regards, Francois

> 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 - 12:00:04 PST
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