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 (
http://q4md-forcefieldtools.org/REDS/), 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
http://www3.interscience.wiley.com/cgi-bin/abstract/109583237/ABSTRACT" 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,
Kamali
On Sat, Dec 7, 2013 at 4:30 PM, FyD <fyd.q4md-forcefieldtools.org> 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 Configuration.py file
>
> > 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:
>
> 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
> http://www3.interscience.wiley.com/cgi-bin/abstract/109583237/ABSTRACT
>
> > - 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:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
>
> > - 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.
> INTRA-MCC1
> See http://www3.interscience.wiley.com/cgi-bin/abstract/109583237/ABSTRACT
>
> 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:
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
>
> regards, Francois
>
>
>
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Received on Mon Dec 09 2013 - 09:00:02 PST
