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
>>>
>>
>>
>>
>>
>
>
>
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Received on Mon Jun 24 2013 - 19:30:02 PDT
