Hello,
On Wed, Apr 21, 2010 at 9:41 PM, ros <ros.servidor.unam.mx> wrote:
> Hello AMBER users!
>
> I am studying non-covalent interactions between ligand/DNA and I've
> read that vdW values are the best to measure and evaluate these
>
DNA is a highly charged molecule (with all of the phosphate groups, etc.).
Therefore, I would argue that electrostatics are strong contributors to
non-covalent interactions between ligand/DNA as well. Compared to vdW,
whose attractive term goes as r^-6, electrostatic interactions go as r^-1,
which is far more long-range. I would argue on this basis that
electrostatics are also important (if not much more so).
> interactions. Where can I get more information of how the vdW values
> are calculated in AMBER? I've tried Amber10 and AmberTools manuals but
> little or no info is available there.
>
Try
http://ambermd.org/Questions/vdwequation.pdf. I pulled this from a
previous post in the mailing list archive:
http://archive.ambermd.org/200902/0235.html .
> Also, what are the units of the
>
> VDWAALS
>
> values in an MD Amber output?
>
If you are referring to the mdout file, all of those values are energies (in
kcal/mol). However, various parameters will not necessarily have units of
energy (the well-depth does, but the radius is in angstroms, as described in
the pdf in the link above).
> For a good evaluation of vdW energy, do I have to make an average of
> all the vdwaals values of all the outputs in a production MD run, or
> just the last value of the last step? What do you recommend?
>
The average is a far more meaningful number (at least very much more so than
an arbitrary final value). It may also be interesting to know the spread of
values that you get, but as is very often the case, what you are trying to
learn dictates what you should be looking for. Typically though, averages
and standard deviations are more interesting than single points for
molecular dynamics (for minimizations, perhaps only the final results are of
interest).
Good luck!
Jason
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Apr 21 2010 - 20:00:02 PDT
