Dear Amber Community,
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.
Thank you all in advance for any help,
Kamali Sripathi
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Received on Sat Jun 15 2013 - 20:30:02 PDT
