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
>
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Thu Apr 22 2010 - 00:30:03 PDT
