Just wanted to comment on the current force field's single strand
predictions. We have done some explicit solvent simulations on single
strand RNAs and saw that the current force field (amber99) is not doing
any good predictions. It looks like that the force field parameters are
optimized to predict the properties of helical structures, not single
strands.
Best regards,
On Thu, 22 Nov 2007, Carlos Simmerling wrote:
> "helical friendly" really should be described as "in love with helices,
> turns everything into one"!
>
> as others have mentioned, use ff99SB or ff03. checked the archives for
> details
> concerning the differences between these two.
>
> On Nov 22, 2007 9:34 AM, Patel, Bhavesh H <bhavesh.h.patel.imperial.ac.uk>
> wrote:
>
> > Hi all,
> >
> > I'm going to be running simulations on the interactions within a
> > enzyme-inhibitor complex and I was wondering which amber force field, FF94
> > or FF99 would be best to use?
> > I know that FF94 is more helical friendly and that ther are some issues
> > with FF99, for example, it can give an inaccurate description of
> > electrostatic interaction between monomers at close distances of approach.
> > Any information will be much appreciated!
> > Thanks
> >
> > *Bhavesh*
> >
>
--
Ilyas Yildirim
---------------------------------------------------------------
= Department of Chemistry - =
= University of Rochester - =
= Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) =
= http://www.pas.rochester.edu/~yildirim/ =
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Received on Sun Nov 25 2007 - 06:07:28 PST
