Dear Francois,
Thank you so much again for your detailed answers.
> 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?
>
No, thank you very much for the offer. I have the PDF and refer to it often
because there are concepts that I'm still learning :)
>
>
> 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.
>
Thanks a lot, Francois, I was hoping that I could do this, but just wanted
to double-check.
I have two final question: from examples on the RED Server (perhaps this is
not applicable to RED Perl or RED Python), it appears that one can also set
the INTRA-MCC constraints to defined values, e.g., sugar carbons to
standard values in the AMBER force field instead of setting the sum of
certain atoms to 0 or to another value. Do you suggest one way over the
other? I understand that it very much depends on one's case, but I was
wondering if you had any thoughts. I was thinking that I might constrain
the charges of some of the sugar atoms that are 5' of the transition-state
pentacovalent phosphate to their values in the AMBER force fields instead
of summing their charges to 0.
I lastly wanted to double-check that the INTER-MCC and INTER-MEQ keywords
are only necessary if one is deriving charges for more than one molecule,
and so would not be applicable in my one-omolecule one-conformation case?
Thank you so much again, and have a great day,
Kamali
>
> regards, Francois
>
>
> > 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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>
--
Kamali Sripathi
PhD Candidate, Medicinal Chemistry
Walter Laboratory
930 North University
Ann Arbor, MI, 48109
ksripath.umich.edu
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Received on Mon Dec 09 2013 - 15:30:02 PST
