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
>>
>
>
>
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jun 23 2013 - 16:30:03 PDT
