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).
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 - 01:00:03 PDT
