Kamali,
please check the PDB file format you use as input...
see
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/readme.txt
regards, Francois
Quoting FyD <fyd.q4md-forcefieldtools.org>:
> Dear Kamali,
>
>> 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:
>
> ok
>
> in the PDB input file:
> ATOM 15 O2P RT0 1 31.511 16.369 54.925 O
> ATOM 16 O5' RT0 6 32.667 14.580 56.630 O
> ATOM 17 P RT0 1 30.934 15.202 55.888 P
> ->
> ATOM 15 O2P RT0 1 31.511 16.369 54.925 O
> ATOM 16 O5' RT0 1 32.667 14.580 56.630 O
> ATOM 17 P RT0 1 30.934 15.202 55.888 P
>
> & look at the residue name generated by R.E.D. Python
>
> You deactivated many keywords in the Project.config file letting the
> defaults to be executed; this is correct. I am glad to see you can do
> the job without a tutorial. We need to provide a tutorial. The
> description of the keywords in the Project.config and Configuration.py
> files is too limited...
>
>> 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.
>
> OPT_Calc = Off1 means you skip the QM job and use the Cartesian
> coordinates from the PDB file to be used in MEP computation. (I am
> really not a big fan of this approach; I would prefer you provide a QM
> job for a Cartesian coordinate set with one imaginary frequency). ok
> for a 'dirt cheap' job ;-) (just my personal opinion)
>
>> I was wondering if there is any documentation for the
>> files generated by RED Python?
>
> Not yet - so far we work on a new version of R.E.D. Python with new
> features...
>
> Just ask for help; sorry for that...
>
>> 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
>
> sm means files related to single molecule charge fit (without intra-mcc)
> ia means files related to charge fitting carried out with intra-mcc
> (because you use 'MOLECULE1-INTRA-MCC1 = 0.0 | 1 4 11 | Keep')
> mm means files related to multiple molecule fit (i.e. number of
> molecules > 1)
>
>> 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?
>
> See
> http://cluster.q4md-forcefieldtools.org/~x/P8824/Data-R.E.D.Server/Mol_m1/Mol-sm_m1-c1.mol2
>
> 1 C4' 30.706000 13.015000 52.944000 CT 1 U01 0.0520 0.8780 ****
>
> 0.0520 is the column of the atomic charge value
> 0.8780 is the column of the atomic polarizability
> (useful for the non-additive FF model)
>
> ---
>
> I do not understand why you use: MOLECULE1-INTRA-MCC1 = 0.0 | 1 4 11 | Keep
> in
> http://cluster.q4md-forcefieldtools.org/~x/P8824/Data-R.E.D.Server/Mol_m1/Mol-ia0_m1-c1.mol2
>
> i.e. 0.6957-0.5092-0.1865=0.0000
>
> then look at the impact of the INTRA-MCC1:
> http://cluster.q4md-forcefieldtools.org/~x/Project/P8824/Data-R.E.D.Server/Mol_m1/Statistics_m1.txt
>
> See the table:
> Charge values for single molecule fit; without (SM) vs with (IA) INTRA-MCC:
> -> the impact seems quite important...
>
> You could also look at :
> - the RRMS values of the corresponding fits.
> - the es*.pdb files to display where the errors are.
> See http://q4md-forcefieldtools.org/RED/resp/#intro
> espdb
> -j PDB-like file with relative residual in the TempFactor field
> esqpotpdb
> -y PDB-like file with input MEP values in the TempFactor field (atomic units)
> esmpotpdb
> -z PDB-like file with MEP values for new charges in TempFactor field
> (atomic units)
>
> let us know if you need more information...
>
> regards, Francois
>
>
>> 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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Received on Wed Dec 11 2013 - 23:00:03 PST
