On Mon, 2014-03-17 at 13:45 +0200, Soumendranath Bhakat wrote:
> Dear Carlos;
>
> Can you please put any scientific article related with your quote " Vacuum
> dynamics could
> introduce terrible artifacts"
This should be readily apparent. DNA and RNA duplexes, for instance,
are inherently unstable and come apart completely in vacuum (see the
first Amber tutorial for a demonstration). Without solvent stabilizing
the negative charges of the phosphate groups, the two strands repel each
other strongly. (Of course, in a vacuum I would not expect the
phosphates to be deprotonated). Also, the very nature of the
"hydrophobic effect," which is responsible for protein folding (i.e.,
the structure of a protein's native state) is driven by solvent entropy
at room temperature. That in itself is strong evidence that the native
state of a protein in solution is drastically different from its native
state in a vacuum. If you look at the papers that introduced the
Merz-Kollman charge scheme used by most of the standard Amber force
fields, you'll see that HF/6-31G* was intentionally used to derive
charges because its neglect of electron correlation overly polarizes the
charge distribution *similar to what you see in solution*. There is
anecdotal evidence everywhere and you can see this assumption used in
many papers even if there is no direct study.
Furthermore, many articles address so-called crystal artifacts which are
attributed to differences between the crystalline environment and
differences in solution. The crystal environment, however, is still
quite close to solution in most respects (it does form in solution,
after all). Vacuum introduces a far greater perturbation than does a
crystal, so I would expect vacuum artifacts to be (much, much) worse
than crystal artifacts.
Long story short: chemistry in solution is _far_ different than
chemistry in a vacuum or in the gas phase. I agree with Carlos that you
should avoid vacuum dynamics for studies intended to take place in
solution.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 17 2014 - 05:30:04 PDT
