Hello!
Thanks to all for your comments!
So, I have to evaluate which Energy has the most relevant contribution in my
specific case: vdW interactions or electrostatic interactions.
How is then, the electrostatic interactions calculated in AMBER?
I will look into MMPBSA also.
What about the van-der-Waals equation (softcore potentials) found in
advanced tutorial 9 in the AMBER site? Is it another way of calculatin vdW
energy?
Thank you again for all your help.
Regards,
Rodrigo.
2010/4/22 <steinbrt.rci.rutgers.edu>
> Hi,
>
> Amber will give you the total vdw-energy of your whole system, including
> ligand, dna and surrounding waters. This will be a very noisy function,
> and hard to extract information about just two molecules interacting. You
> may want to consider using the MMPBSA or Ambers decomposision approach for
> what you describe.
>
> Kind Regards,
>
> Thomas
>
> On Wed, April 21, 2010 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
> > 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.
> >
> > Also, what are the units of the
> >
> > VDWAALS
> >
> > values in an MD Amber output?
> >
> > 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?
> >
> > Thank you for your help!
> >
> > Have a great day.
> >
> > Rodrigo
> >
> > ------------------------
> > Ph. D. student
> > Instituto de Quimica
> > UNAM - México
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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>
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Received on Thu Apr 22 2010 - 09:00:03 PDT
