AMBER Archive (2008)

Subject: Re: AMBER: Is there any way I can extract the potential energy of the solute with the solvent instead of the total energy in Amber?

From: Barbault Florent (florent.barbault_at_paris7.jussieu.fr)
Date: Sat Sep 20 2008 - 15:40:34 CDT

Hello,

MMPBSA is suited for this sort of calculations. You will need a
topology of your solute (without water box). You might have a look on
the manual for making your script.

Hope this will help you
Regards
Florent Barbault

On Sat, 20 Sep 2008 16:01:59 -0400
  "Zhao, Zhen (zhaozh)" <zhaozh_at_ucmail.uc.edu> wrote:
> Hi, all
>
> I wonder if there is a command in Amber that allows me to extract
>the potential energy of a solute (for example, an ion) with all the
>water molecules? Since the total energy in the output file includes
>the water - water interactions too.
>
> I understand I can do two calculations, with the solute and without
>the solute and substract the two total energies. But I think that is
>not a good way since I am substract two large numbers where the
>errors might be bigger that the difference.
>
> Thanks for your kind help!
>
> Sincerely
>
> Zhen
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