Hi Brian, thank you for comments!
> I've thought about this briefly myself. I'm not an expert, but I can't
> think of any obvious problems with the link atom procedure. However, it
> might be interesting to check exactly which MM dihedral terms are kept also
> (e.g. C4' - C3' - C2' - C1').
It is really interesting (C4'-C3'-C2'-C1'), I will try to check this.
> What will almost definitely be problematic is the partial charges on the MM
> atoms, since the ring is very unlikely to be partitioned into regions of
> integer charge.
Yes, this is a common problem and I keep it in mind)
> What kind of molecule/fragment do you fit?
Nucleotide, in this particular case.
--
Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
web: http://enzyme.fbb.msu.ru/
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Received on Sat Jan 28 2012 - 02:00:02 PST
