[AMBER] vdW question.

From: ros <ros.servidor.unam.mx>
Date: Wed, 21 Apr 2010 20:41:38 -0500

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


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.


Ph. D. student
Instituto de Quimica
UNAM - México

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Received on Wed Apr 21 2010 - 19:00:03 PDT
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