Dear Francois,
Thank you so much for your detailed responses. I'm sorry, but I do have a
few follow-up questions.
On Tue, Jun 25, 2013 at 3:55 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Kamali,
>
> 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.
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?
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? 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?
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?
Thank you so much again, Francois, and I'm very sorry for the long email.
Have a great day,
Kamali
> Do not hesitate to ask more questions if something is not clear...
>
> 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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Received on Tue Jun 25 2013 - 06:00:03 PDT
