Dear Francois,
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?
Thank you so much again, and have a great day,
Kamali
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 18 2013 - 13:30:04 PDT
