Hi Dave,
It is the free energy predictions on 2 systems I have been working on. One
part of the thermodynamic cycle is the single strand part. I have started
with 10 conformers and done 1 ns simulation for each of them. The TI
prediction is way off from the experimental predictions.
Then, I have only used the A-form conformations with backbone
dihedrals restrained to the initial structures. For both 2 systems, TI
predictions are pretty good with the experimental results (free energy
results).
Is 1 ns long enough? Of course it is not. But when the structures are
started with A-form without restraints, it deforms itself to some other
conformations. I did not run the sim.s for a long time (let's say 100
ns) to see how much time is spends on the preferred conformations (which I
cannot do in TI Approach as it is too long to do).
I do not want to go into detail of these systems, but the current amber
force field does not look like working good on single strands (at least
for tetramers). Now, the question is, do these tetramer single strand RNAs
have A-form conformations? Previous works say that single strands have
some prefered conformations which look like A-form. I will do some single
strand tetramer NMR work to see if the conformations look like A-form.
My understanding of force field development is that it tries to predict
the helical structures as good as it is seen experimentally, which means
that the predictions are good for helices.
Best regards,
On Fri, 23 Nov 2007, David A. Case wrote:
> On Thu, Nov 22, 2007, Ilyas Yildirim wrote:
>
> > 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.
>
> Just curious: what are the bad predictions? How do you know what the right
> answer is, and are you sure that your calculations are converged?
>
> ....dac
>
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--
Ilyas Yildirim
---------------------------------------------------------------
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= 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 - 06:07:44 PST
