Re: [AMBER] vdW question.

From: Kevin Hauser <>
Date: Wed, 21 Apr 2010 23:26:50 -0400


In agreement with Jason's comments, electrostatic interactions ought to be
"more" important than van der Waals interactions, however your system may
have the peculiar property that vdw is indeed a major player. I would use
VMD ( to look at the system in detail.
The website contains tutorials on how to load the molecule, create
representations, etc. Once you've got the basics of this down, then I would
do the following:

1.) with the molecule loaded, create a representation with the selection
"within 5 of nucleic" (this will make sense after playing with VMD and
studying the tutorial) using "lines" drawing method and another
representation "nucleic" using "licorice" drawing method.
2.) visually inspect the "within 5 of nucleic"-to-"nucleic" interactions.
This will give you a good idea of what interactions YOU think are

"within 5 of nucleic" translates to "all atoms within 5 angstroms of nucleic

Without visual inspection, it will be difficult, if not impossible, to
determine what's important in your system.

As an added note, VMD is very powerful for quick analysis. You could load a
trajectory, specify a distance between two atoms, allow the trajectory to
traverse, and using the Graphical Representations window, actually see a
mini-plot of the distance during the trajectory, but I digress.

Simmerling, Cheatham, Case and others from the AMBER team have published a
plethora of DNA-related articles whose analysis and discussions could be
very useful in your endeavors.

Good luck,

On Wed, Apr 21, 2010 at 10:29 PM, Jason Swails <>wrote:

> Hello,
> On Wed, Apr 21, 2010 at 9:41 PM, ros <> 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 I pulled this from a
> previous post in the mailing list archive:
> .
> > Also, what are the units of the
> >
> >
> > 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
> _______________________________________________
> AMBER mailing list

-- - -
Kevin Eduard Hauser
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
(631) 913.3194
(561) 635.1848
AMBER mailing list
Received on Wed Apr 21 2010 - 20:30:03 PDT
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