Dear Kamali,
> I have one final question for now: in a previous message, you mentioned
> that I should provide a QM output (with one imaginary
> frequency) as input for RED Python. Does this mean that I should leave the
> imaginary frequency calculations of the form, e.g.,
> *Frequencies -- xxxx.xxxx yyyy.yyyy zzzz.zzzz* in the QM output, but
> delete all the real frequencies as specified here:
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#6?
First characterize this TS using the QM program of your choice; then
once you got it you can 'prepare' the QM output so that it is
correctly recognized by R.E.D.
See
http://q4md-forcefieldtools.org/REDS/faq.php#15
regards, Francois
> On Fri, Dec 13, 2013 at 10:30 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Kamali,
>>
>> > I also agree that I shouldn't use these results for my final
>> calculations;
>> > I just used the OPT_Calc = "OFF1" option as part of a "practice run" so
>> > that I could see how to successfully submit a job to R.E.D Python and how
>> > the outputs would look.
>> >
>> > In a previous message you also asked why I used the INTRA-MCC constraints
>> > that I did: this was also part of the "practice". I chose atoms to
>> > constrain that made sense to me, and I just wanted to see what would
>> > happen.
>>
>> You constrain atoms (using intra-mcc) that needs to be; for instance
>> to generate a molecular fragment from a whole molecule; in your case
>> you study a TS so I do not think you need to generate a molecular
>> fragment (except if you do want to connect it to a larger entity).
>>
>> > I actually don't think I need to constrain any atoms beyond the
>> > default setting; is it possible to also use defaults for INTRA-MCC?
>>
>> No
>>
>> > Maybe I should start a different thread for this question, but I have
>> > actually tried to submit job P8902 with OPT_Calc = OFF and providing my
>> own
>> > QM output. However, I've gotten errors in the R.E.D.-
>> > Server-14651.master0.q4md-forcefieldtools.org file:
>>
>> ok I looked at the minimum you provided in the P8902 job. This is not
>> the TS you are interested in... please compare your PDB input file and
>> this QM output i.e. the last set of Cartesian coordinates...
>>
>> > *...*
>> > *Reading JOB1*.log for molecule : 1*
>> > *Find "Normal termination of Gaussian"*
>> > *Find "Normal termination of Gaussian"*
>> > *Find "Stationary point found"*
>> > *Find "Standard orientation"*
>> > *Element in JOB1 is not the same with PDB*
>> > *Find big error in log : /home/u0263B7BZ/P8902/JOB1-gau_m1-1.log*
>> > *JOB1*.log is not correct , can not continue......*
>> > *Information of end*
>> > *Time : Wed Dec 11 22:26:46 CET 2013*
>> >
>> > But to me the JOB1-gau_m1-1.log looks fine. Did I have to modify my QM
>> > output (similar to what one must do for R.E.D Server Perl)?
>>
>> try removing the Frequency job from the Mol_red1.log file as described
>> in red color at:
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#6
>> (see -4-The last step consists of checking and preparing the P2N and
>> QM output files for the R.E.D. III.x execution)
>>
>> >> In these conditions _the key_ is the definition of the atom
>> >> connectivities from this PDB file (atom typing & FF parameters are
>> >> based on these atom connectivities). You have C-H bonds with 1.5 Angs
>> >> length in your PDB input file. Are you sure an atom connectivity is
>> >> created in this case (VMD does not...)?
>> >
>> > You're correct; those bond lengths should be fixed, and I will do that
>> > before the next time I submit my structure.
>> >
>> >
>> >> Your best bet here (because RED Python computes atom connectivities
>> >> after the geometry optimization step and you skip this step...) is to
>> >> provide the atom connectivities *YOU* want in the PDB input file and
>> >> *prevent* their computation.
>> >>
>> >> See
>> >>
>> http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Project.config
>> >> MOLECULE1-CALCONECT = OFF
>> >>
>> >> then you need to carefully think which atom types you want: obviously
>> >> two CT-H1 or CT-H2 bonds (CT, H1, H2 are atom types) cannot have two
>> >> different equilibrium values; i.e. ~1.0 and ~1.5 Angs -> a new atom
>> >> type has to be created...
>> >>
>> >> Moreover your phosphor atom has 5 bonds I would set up a new atom type
>> >> for it...
>> >
>> > Thank you for the suggestion, Francois. But I am wondering if the new
>> > phosphorus atom type is necessary? I ask because it is possible in nature
>> > for phosphorus to form 5 bonds.
>>
>> look at the atom type definition in the Amber FF for the phosphorus
>> atom in the phosphate group; it is related to this NA structure:
>> http://en.wikipedia.org/wiki/File:DNA_chemical_structure.svg
>>
>> >> Finally I really hope the Cartesian coordinates you have were checked
>> >> by QM: once again better providing a QM output (with one imaginary
>> >> frequency) as input for RED Python...
>> >
>> > For job P8902, I used Gaussian09 with these options:
>> >
>> > #P hf/6-31G* Opt=(Tight,CalcFC) Freq SCF(Conver=8) Test
>> >
>> > I tried to answer this question on my own, but I got confused: why do I
>> > need imaginary frequencies for my calculations, and why only just one?
>>
>> See http://www.gaussian.com/g_tech/g_ur/k_opt.htm
>> & use the QST2 or QST3 keyword.
>>
>> one imaginary frequency for a TS is what I learned: I think you need
>> to read about that ;-)
>>
>> regards, Francois
>>
>>
>> >> Quoting FyD <fyd.q4md-forcefieldtools.org>:
>> >>
>> >> > 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 Mon Dec 16 2013 - 02:00:03 PST
