Dear Francois,
Thank you so much for your detailed answers and your willingness to answer
my questions!
I have just one more: I'd like to run a multiple conformation run (I have
the C3'endo-syn, C3'endo-anti, C2'endo-syn and C2'endo-anti conformations
of my nucleoside), but I am wondering if there is any documentation on how
to concatenate the p2n files? The concatenated one I saw from the tutorial
seemed to have a different header than the normal ones, and I was just
wondering if I modify the header by hand after concatenating the p2n files,
or if there is another way to do this.
Thank you so much for all your help, Francois, and have a great night,
Kamali
On Wed, Jun 26, 2013 at 4:43 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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.
> >> >>>>>
> >>
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
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Received on Wed Jun 26 2013 - 20:30:02 PDT
