Dear Kamali,
> On Tue, Jun 25, 2013 at 3:55 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>>
>> For a listing of R.E.D. outputs; see PDF files:
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
>> & its PDF file:
>>
>> http://q4md-forcefieldtools.org/Tutorial/P2N/Central-frag-Pept/listing-1mol.pdf
>> or
>> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
>> & its PDF file:
>> http://q4md-forcefieldtools.org/Tutorial/P2N/All-frag-Pept/listing-6mol.pdf
>>
>> You can find more examples in the tutorials...
>>
>> Now about these 'stat' files; no documentation is available: sorry...
>>
>> stat-QMSOFT_m1: charge values (ESP, Mulliken, Lowdin (if available))
>> extracted from the QM prog., GAMESS, Firefly or Gaussian, i.e. from
>> the JOB2....log file(s)); to be used for comparison with RESP or ESP
>> charges (i.e. with the final R.E.D. output).
>>
>> stat-RESP-FITab_m1; output for the RESP inputs: stat-input-a_m1 &
>> stat-input-b_m1
>>
>> stat-input-a_m1: qwt= 0 & chemical equivalencing is canceled; this
>> means you should get the _exact_ ESP charge values generated by the QM
>> prog. (i.e. stat-QMSOFT_m1) -> kinf of 'cross' comparison.
>>
>> stat-RESP-FIT_m1: qwt= 0.0005 & chemical equivalencing is canceled;
>> for comparison with classical RESP charge values (or with the final
>> R.E.D. output).
>
> Why is chemical equivalencing cancelled, and why is it turned on again
> before stat-input-b_m1 is processed? I can see that chemical equivalencing
> is turned on for stat-input-b_m1, because one of my molecules is a
> nucleotide: the charges of the nonbridging oxygens are not identical in the
> "Charges input-a - Molecule 1 - MOLECULE" portion of
> the stat-RESP-FITab_m1, but these two charges become identical for the
> "Charges input-b - Molecule 1 - MOLECULE" portion.
- the QM program generates ESP charges without chemical equivalencing
- charge equivalencing for chemically equivalent atoms is required for
MD simulation, See
http://q4md-forcefieldtools.org/RED/reference.php
then
http://pubs.acs.org/doi/abs/10.1021/j100142a004 page 10271
last paragraph before "Methods"
This means:
-1- when the goal is to generate a FF library to be involved in MD,
charge equivalencing _has_ to be applied during charge derivation.
-2- when the goal is to study the impact of charge equivalencing for
instance on the RRMS value of the charge fitting step and/or to
compare charge values with these generated by the QM program charge
equivalencing can be canceled.
> I chose the RESP-A1 method for generating RESP charges; I was wondering why
> there is no qwt=0.001 step? Or is that what the stat-input-a_m1 input does?
stat-input-a_m1 is generated by the statistics module of R.E.D.: this
corresponds to case -2- above; to perform charge value comparison
for charge derivation used in FF library building for MD simulation
(case -1- above) the RESP inputs are input1_m1 & input2_m1 where
charge equivalencing is applied.
> I am planning on using these generated charges in free energy calculations;
> do you know by any chance how robust the charges would be in such
> simulations?
I would do a literature search here being aware that many factors
affect charge values; among them the impact of the conformation on the
charge values is important. See the R.E.D. article and articles cited
herein.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
You could vary algo. used in MEP computation and/or the charge fitting
procedure; i.e. not use only the RESP-A1 charge model.
you also could modify the source code of R.E.D. and create your own
approach (QM theory level)...
> My jobs only finished successfully if I submitted them to the
> RED Server using Mode 1, and I have only ever uploaded the C3' endo
> conformation. Do you have any suggestions of ways to generate more
> appropriate libraries for free energy calculations?
See
http://q4md-forcefieldtools.org/REDS/faq.php#5
what is PXXXX R.E.D. Server job name?
you could vary the conformation of your molecule and consider the
different conformations of this molecule as (1) conformations to be
involved in multiple conformation charge derivation (where the
conformations are concatenated in a single P2N file ) and (2)
different molecules (so different P2N files) to be involved in
multiple molecule charge derivation.
> My last question: I have been getting different spin multiplicities when I
> generate a P2N file using the Ante_RED 2.0 server versus when I generate a
> .gjf file using GaussView, and my jobs only run successfully when I change
> the spin multiplicity in the P2N files to the ones from GaussView. Is it
> all right to do this?
Ante_R.E.D. generates a spin multiplicity = 1 and the user has always
to check this spin multiplicity (as well as the total charge) of the
molecular system before running R.E.D.
(BTW R.E.D. python generates .gjf file instead of .com by now)
> Thank you so much again, Francois, and I'm very sorry for the long email.
> Have a great day,
you can ask as many questions as you wish ;-)
regards, Francois
>> > As I was going through the RED procedure, I did come up with one
>> question:
>> >
>> > I'm wondering if you can direct me to some sort of documentation that
>> > describes the different outputs generated by RED IV. Although tutorials 1
>> > and 3 are very helpful, I have not been able to find explanations for
>> files
>> > like stat-RESP-FITab_m1 and stat-RESP-FIT_m1. For these two files
>> > specifically, I'm wondering what the contents of each file are.
>>
>> > On Mon, Jun 24, 2013 at 10:01 PM, Kamali Sripathi <ksripath.umich.edu
>> >wrote:
>> >
>> >> Dear Francois,
>> >>
>> >> Please disregard my previous questions. I have found a way to generate
>> at
>> >> least some of my desired libraries that avoids the problems that I
>> >> mentioned before. Thank you very much for your help, and have a good
>> night,
>> >>
>> >> Kamali
>> >>
>> >>
>> >> On Sun, Jun 23, 2013 at 7:10 PM, Kamali Sripathi <ksripath.umich.edu
>> >wrote:
>> >>
>> >>> Dear Francois,
>> >>>
>> >>> I'm very sorry, but I have some follow-up questions: I've been trying
>> to
>> >>> pass through two different input files (both of the N9-methyl adenoisne
>> >>> that I discussed earlier) through Gaussian: one I generated using the
>> >>> Ante_RED 2.0 server, while the other I generated using GaussView for
>> >>> comparison. Lately, I've always been getting the same error:
>> >>>
>> >>> *...*
>> >>> *KE= 5.037035512626D+02 PE=-2.406763450321D+03 EE= 7.853661184581D+02*
>> >>> * Annihilation of the first spin contaminant:*
>> >>> * S**2 before annihilation 0.9698, after 0.7817*
>> >>> * Convergence failure -- run terminated.*
>> >>> * Error termination via Lnk1e in /usr/caen/gaussian-09revc/g09/l502.exe
>> >>> at Sun Jun 23 18:07:25 2013.*
>> >>> * Job cpu time: 0 days 0 hours 7 minutes 45.4 seconds.*
>> >>> * File lengths (MBytes): RWF= 36 Int= 0 D2E= 0 Chk=
>> >>> 2 Scr= 1*
>> >>>
>> >>> (the complete Gaussian output file, RAP_N9Methyl_from_Ante_RED_4.out,
>> is
>> >>> attached for your reference). The input file generated by GaussView and
>> >>> Ante_RED are also attached: RAP_N9methyl_from_GaussView_4.gjf and
>> >>> RAP_N9Methyl_from_Ante_RED_4.com.txt, respectively. Because I
>> initially
>> >>> started my parameterization using Gaussian and antechamber, I put the
>> same
>> >>> specific comments at the beginning of
>> RAP_N9methyl_from_GaussView_4.gjf
>> >>> and RAP_N9Methyl_from_Ante_RED_4.com.txt. I tried Gaussian runs
>> >>> of RAP_N9Methyl_from_Ante_RED_4.com.txt with Link1 information as
>> well,
>> >>> but ended up taking that information out because I kept getting
>> errors. I
>> >>> know that my N9-methyl-adenosine fragment can't be passed through the
>> >>> RED-IV server, but I'd like to try to at least get Gaussian outputs for
>> >>> these. I did succeed in getting Gaussian outputs for
>> >>> the N9-methyl-adenosine using GaussView to generate the input, but
>> it's
>> >>> not working for me now for some reason.
>> >>>
>> >>> I also noticed that the spin multiplicity for the Gaussian inputs
>> >>> generated by GaussView and Ante_RED differed: The multiplicity for the
>> >>> GaussView file was 2, while the multiplicity for the Ante_RED file was
>> 1.
>> >>> In the files that I've attached, the multiplicity in the Ante_RED file
>> >>> ( RAP_N9Methyl_from_Ante_RED_4.com) has been changed from 1 to 2 to
>> avoid
>> >>> Gaussian errors regarding multiplicity. Can you please tell me why
>> there is
>> >>> this difference between Gaussian and Ante_RED?
>> >>>
>> >>> Thank you very much for all your help, and I'm sorry for al the
>> >>> questions. Have a great night,
>> >>>
>> >>> Kamali
>> >>>
>> >>>
>> >>> On Sun, Jun 23, 2013 at 8:06 AM, Kamali Sripathi <ksripath.umich.edu
>> >wrote:
>> >>>
>> >>>> Dear Francois,
>> >>>>
>> >>>> Thank you very much for your reply, and I'm sorry for my late one. The
>> >>>> reason I would like to keep the base and sugar charges unperturbed is
>> >>>> because my collaborator and I are conducting constant pH simulations,
>> and
>> >>>> every atom affected by protonation would have to be treated as a
>> hybrid
>> >>>> atom, increasing the complexity of the group to be titrated.
>> >>>>
>> >>>> I believe I have successfully run the Ante_RED program to generate an
>> >>>> input for Gaussian 09. As I understand it, this input can be used
>> with a
>> >>>> standalone version of Gaussian to generate the Gaussian output for
>> the RED
>> >>>> IV server. Is this correct? I was under the impression RED IV could
>> also
>> >>>> use Gaussian to run geometry optimization for me, but I tried to
>> submit a
>> >>>> job with only the .com file from Ante_RED and kept getting errors.
>> >>>>
>> >>>> When I try running standalone Gaussian using the input generated from
>> >>>> Ante_RED, I get this error in the output:
>> >>>>
>> >>>> * The combination of multiplicity 1 and 79 electrons is
>> impossible.*
>> >>>> *
>> >>>> *
>> >>>> I've seen from the mailing list archives that this sometimes happens
>> for
>> >>>> fragments of molecules. As I've stated in previous messages in
>> >>>> this thread,
>> >>>> at this point I'm trying to generate a library for simply the
>> >>>> N9-methyl-N1-protonated adenine, in an attempt to keep the sugar and
>> >>>> phosphate charges the same. Is there any way that I can submit the
>> base
>> >>>> alone through the server?
>> >>>>
>> >>>> I have one more question, just to confirm: the Ante_RED program
>> >>>> automatically reorders the atoms from the input PDB file in the
>> optimal
>> >>>> order for generation of the P2N file, is that right? In the tutorials
>> I've
>> >>>> read that sometimes one has to manually re-order or re-name certain
>> atoms,
>> >>>> but I'm a little confused as to when I have to do that.
>> >>>>
>> >>>> Thank you very much, and have a great day,
>> >>>>
>> >>>> Kamali
>> >>>>
>> >>>>
>> >>>>
>> >>>> On Wed, Jun 19, 2013 at 4:13 AM, FyD <fyd.q4md-forcefieldtools.org
>> >wrote:
>> >>>>
>> >>>>> Dear Kamali,
>> >>>>>
>> >>>>> > Thank you for this reference. One of my collaborators actually
>> tried
>> >>>>> this
>> >>>>> > server; we came up with the question of how to keep, e.g. in the
>> case
>> >>>>> of
>> >>>>> > N1-protonated adenine, the charges of the base and the sugar
>> >>>>> essentially
>> >>>>> > the same as those for canonical adenine while only changing the
>> >>>>> charges of
>> >>>>> > the base atoms. Would this be possible with the RED server? Should
>> I
>> >>>>> > instead use the organic molecule tutorial rather than the
>> nucleoside
>> >>>>> one?
>> >>>>>
>> >>>>> - Changing the formal (total) charge of a molecule should strongly
>> >>>>> affect the partial (atomic) charges.
>> >>>>>
>> >>>>> You can easily test that with R.E.D. Server; simple prepare two P2N
>> >>>>> files: for the reference and the modified structure, and run a charge
>> >>>>> derivation and FF library building procedure for these two molecules.
>> >>>>>
>> >>>>> - NucleoSIDES are used with dimethylphosphate to generate nucleoTIDE
>> >>>>> fragments:
>> >>>>> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26
>> >>>>> as well as:
>> >>>>> http://onlinelibrary.wiley.com/doi/10.1002/jcc.540161106/abstract
>> >>>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
>> >>>>> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/figure/F4/
>> >>>>>
>> >>>>> - You can also provide the 'PXXXX' R.E.D. Server job name in the
>> email
>> >>>>> sent to the q4md-fft (or amber) mailing list so that we can more
>> >>>>> easily assist you.
>> >>>>>
>> >>>>> - You can also request a private assistance from the R.E.D. Server
>> web
>> >>>>> site.
>> >>>>> See http://q4md-forcefieldtools.org/REDS/faq.php#5
>> >>>>>
>> >>>>> regards, Francois
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> > On Tue, Jun 18, 2013 at 3:31 AM, FyD <fyd.q4md-forcefieldtools.org
>> >
>> >>>>> wrote:
>> >>>>> >
>> >>>>> >> Dear Kamali Sripathi,
>> >>>>> >>
>> >>>>> >> See R.E.D. Server to derive charges and build FF library for
>> modified
>> >>>>> >> residues.
>> >>>>> >>
>> >>>>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
>> >>>>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#26
>> >>>>> >> &
>> >>>>> >> http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#27
>> >>>>> >>
>> >>>>> >> http://q4md-forcefieldtools.org/REDS/
>> >>>>> >>
>> >>>>> >> regards, Francois
>> >>>>> >>
>> >>>>> >>
>> >>>>> >> > I am using antechamber to optimize geometry and generate RESP
>> >>>>> partial
>> >>>>> >> > charges for modified nucleosides. My first try is re-generating
>> >>>>> charges
>> >>>>> >> for
>> >>>>> >> > N1-protonated adenine. Antechamber appears to have run
>> >>>>> successfully -- I
>> >>>>> >> > submitted the job to a cluster, and so was unable to monitor the
>> >>>>> output.
>> >>>>> >> > None of the output files have any warnings in them or appear to
>> be
>> >>>>> >> > incomplete, so I believe that the job ran successfully. Is that
>> a
>> >>>>> safe
>> >>>>> >> > assumption?
>> >>>>> >> >
>> >>>>> >> > I also have a second question: I've been assigning atom
>> >>>>> descriptions
>> >>>>> >> based
>> >>>>> >> > on all_nuc94.in to the prepc file that I generated in
>> preparation
>> >>>>> for
>> >>>>> >> > making a tree, and it looks like the protonated N1 has the type
>> >>>>> "NA",
>> >>>>> >> which
>> >>>>> >> > has the description "sp2 N in 5 memb.ring w/H atom (HIS)" I'm
>> >>>>> thinking
>> >>>>> >> the
>> >>>>> >> > protonation is keeping this atom from being given the NC atom
>> type
>> >>>>> ("sp2
>> >>>>> >> N
>> >>>>> >> > in 6 memb.ring w/LP (ADE,GUA)" -- I'm guessing "LP" means "Lone
>> >>>>> Pair",
>> >>>>> >> > which would of course be wrong in my case). I'm just wondering
>> how
>> >>>>> much
>> >>>>> >> > emphasis I should place on the description? I ask because I have
>> >>>>> one
>> >>>>> >> > hydrogen described as "H arom.at C with 2 elctrwd. gr,+HCOO
>> >>>>> group",
>> >>>>> >> when I
>> >>>>> >> > definitely don't have a carboxylic acid in my system, as well
>> as a
>> >>>>> few
>> >>>>> >> > carbons that are described as being in pyrimidines. I'm just
>> >>>>> wondering if
>> >>>>> >> > this means that there is something wrong with my calculations,
>> or
>> >>>>> if
>> >>>>> >> these
>> >>>>> >> > discrepancies are something I can overlook. A lot of the other
>> >>>>> atom types
>> >>>>> >> > and their accompanying descriptions are spot-on, which is what
>> got
>> >>>>> me
>> >>>>> >> > worrying about the inconsistencies.
>> >>>>>
>>
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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>
>
F.-Y. Dupradeau
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Received on Wed Jun 26 2013 - 02:00:02 PDT
