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 Wed Jun 19 2013 - 01:30:02 PDT
