Dear Kamali,
> I have just one more:
until the next one ;-)
> 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?
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php
&
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#EXAMPLE-P2N-FILE
in Cieplak et al. JCC 1995 the authors used 'only' two conformation
RESP fit...
> 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.
header changes in particular when one needs to specify constraints
during the charge fitting step.
regards, Francois
> 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
Received on Thu Jun 27 2013 - 07:00:02 PDT
