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 - 21:30:03 PST
