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 Sun Jun 23 2013 - 05:30:02 PDT
