Hi Aneesh,
you can use mm_pbsa to quantify the interaction between the drug and
the DNA. Also, you can alternativelly use NAMDEnergy script in VMD or
you can use AMBERENERGY, my own program (very simple, but useful. Send
me an e-mail offline if you want to try). mm-pbsa works pretty well
and allows one to quantify the solvation contribution to the binding
energy (usually relevant when a DNA molecule is involved). There is a
tutorial on how to use mm_pbsa in amber website.
Hope this helps,
--alessandro
On Mon, Nov 1, 2010 at 3:04 AM, aneesh cna <aneeshcna.gmail.com> wrote:
> Dear Amber users,
>
> I am studying DNA-drug interaction using Amber 9.0
> package. From the literature I came to know that the drug have both
> hydrophobic as well as electrostatic interaction with DNA and hydrophobic
> interaction is dominant over electrostatics. How can I quantify these two
> interactions from my simulation data?
>
>
> Thanks in advance
>
> Sincerely
> Aneesh
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>
--
[ ]s
--alessandro
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Received on Mon Nov 01 2010 - 10:00:02 PDT
