AMBER Archive (2006)

Subject: Re: AMBER: base-base interaction

From: Carlos Simmerling (carlos.simmerling_at_stonybrook.edu)
Date: Fri Jan 13 2006 - 12:07:57 CST

ptraj doesn't calculate energies.
you can do energy decomposition in Amber if
you are doing mmpbsa analysis (see the manual and
look for idecomp).

Douali, Latifa wrote:

>Hi all,
>
>Is there a way to calculate base-base interactions in DNA or RNA
>duplexes using ptraj module of AMBER?
>I would appreciate if somebody could give me some information on how we
>can do that.
>
>Thank you in advance.
>
>Latifa
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