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 - 01:00:02 PDT
