Re: [AMBER] best Generalized Born solvation model for intrinsically disordered peptides

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Thu, 5 Sep 2013 08:48:46 -0600

Hi,

On Tue, Sep 3, 2013 at 2:55 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> how long you have been running? 20ns? if yes, I suggest to run much longer
> like microsecond. For a small peptide, getting this long simulation isn't

Just to expand on Hai's point a bit, one of the major issues when
comparing implicit solvent to explicit solvent runs is that in
explicit solvent, conformational sampling is typically much slower
than in implicit solvent (due to friction, explicit solvent
rearrangement, etc). You haven't said how long the explicit solvent
runs are, but you need to be sure that the structural properties in
each simulation are reasonably converged before you compare them, and
if you've only run explicit solvent as much as your implicit (17 ns)
chances are the run is not converged.

> the parameters quoted at the end of the message. In contrast, when using
> igb 7 the peptide has some helical propensity but is mostly
> unstructured (helical and random coil conformations are in equilibrium).

This result may not necessarily be wrong, but as Carlos said the GB
neck (igb=7) model has a tendency to destabilize hydrogen bonding so
be wary of these results. For more on this see:

Roe, D.R.; Okur, A.; Wickstrom, L.; Hornak, V.; Simmerling, C., J.
Phys. Chem. B, 2007, 111, 18461857.
Shell, M.S.; Ritterson, R.; Dill, K.A., J. Phys. Chem. B., 2008, 112, 6878-6886.

-Dan

-- 
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Thu Sep 05 2013 - 08:00:03 PDT
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