Dear Francois,
I have been trying a few things out with my transition state structure of
RNA cleavage, and I had a few follow-up questions. My questions are
regarding my job P8824:
Following your suggestion in the private communication (when we first
talked about this structure), for this job I just ran the PDB through the
RED Server Dev. with the option OPT_Calc = Off1 in the Project.config file,
as a practice run. I was wondering if there is any documentation for the
files generated by RED Python? I found two types of files in the
P8824/Data-R.E.D.Server/Mol_m1 folder: *sm* files (which I know are files
containing intra-molecular charge constraints) and the *ia*: what does the
*ia* mean? I also have two .mol2 files: Mol-ia0_m1-c1.mol2
and Mol-sm_m1-c1.mol2, but these files appear to have two columns of
charges rather than one next to the rightmost **** column. Could you tell
me which column is the correct one for charges, or alternatively point me
to documentation that answers my questions?
Thank you very much, and have a great day,
Kamali
On Tue, Dec 10, 2013 at 8:12 AM, Kamali Sripathi <ksripath.umich.edu> wrote:
> 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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>
>
>
>
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Received on Wed Dec 11 2013 - 13:00:03 PST
