On Sat, Jan 28, 2012 at 4:33 AM, Dmitry Nilov <nilovdm.gmail.com> wrote:
> 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.
>
> No doubt a nucleotide is an acceptable charge model, but how do you
constrain the charges on that part of the ring to be integer? The charge
on the front "methylene" groups (the link atom is effectively hydrogen I
believe) will fluctuate during a simulation and probably depend on the
phosphate configuration, so it doesn't seem trivial to me to lock down
those charges during the RESP fit. Perhaps just trying it and seeing what
happens is the best avenue here.
> --
> Dmitry Nilov
> Faculty of Bioengineering and Bioinformatics,
> Lomonosov Moscow State University
> web: http://enzyme.fbb.msu.ru/
>
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Sat Jan 28 2012 - 14:00:02 PST
