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 - 00:00:02 PST
