Dear 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.
Thank you very much, and have a great night,
Kamali
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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>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>
>
>
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Received on Mon Jun 24 2013 - 20:30:03 PDT
