Dear Francois,
Thank you very much for the detailed information, and I'm sorry for the
confusion. I would have mentioned that I had questions about a topic
related to our private discussion, but I didn't want you to have to look up
that communication, and so I tried to start a new thread :) Looking back, I
see that my initial email in this thread was unfortunately less clear than
I intended.
I will try the protocol you suggested, but I think it would be better for
me to use the RESP-A1 charge type because I'm working with RNA rather than
carbohydrates, and using AMBER10 for my simulations.
Thank you very much again, and have a great day,
Kamali
On Tue, Dec 10, 2013 at 2:52 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Kamali,
>
> > 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 :)
>
> Yes a looot to learn in this work...
>
> > 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 would constrain hydrogen atoms (only these in the methylene & methyl
> groups, using the 'F' flag in the intra-mcc to keep them in the FF
> lib) _only_ if you use the GLYCAM force field. So the 'RESP-C2' charge
> model (to be provided in the Configuration.py file to overwrite the
> default RESP-A1):
> see http://q4md-forcefieldtools.org/REDS-Development/popup/popkeyword.php
>
> Here once again I would use INTRA-MCC1; in general one always uses
> INTRA-MCC1 except when one realizes that some atoms are not
> equivalenced as they should be ;-)
>
> > 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.
>
> oh oh I got it: You continue the discussion from the private assistance...
> Not easy to follow you. In your case I would:
> -1 characterize the TS using the QM program of your choice
> -2 run RED Python using CHR_TYP = "RESP-C2", OPT_Calc = "Off" &
> MEPCHR_Calc = "On" using the QM log file & PDB file as inputs
> -3 study what you get: here you will be able to:
> - check the atom connectivities generated in the mol3 file
> - re-run RED Python using Re_Fit = "On" (i.e. upload/provide the
> entire/previous RED Python job in the archive)
> - provide new FF parameters in the frcmod.user (see the
> frcmod.unknown file generated in the previous job) in the archive file
> See
> http://q4md-forcefieldtools.org/REDS-Development/RED-Server-demo1.php
>
> http://q4md-forcefieldtools.org/REDS-Development/popup/poptestcase.php
>
> http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/frcmod.user
> - provide new FF atom types in the Project.config file for key atom
> center(s)
> MOLECULE1-ATMTYPE = ...
> (here you can load your own FF as input to R.E.D. Python)
>
> When ready just request a private assistance and provide the PXXXX
> R.E.D. Server job name in the body of your email.
>
> > 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?
>
> Yes INTRA means within a molecule; INTER means between molecules.
>
> regards, Francois
>
>
> >> 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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Received on Tue Dec 10 2013 - 05:30:02 PST
