Hi Kirtana,
you can use MM-PBSA for that purpose. There is a tutorial on how to use it
on the Amber page plus some examples in the $AMBERHOME/src/mmpbsa
directory. But note that it will be very difficult to get the correct
ensemble for your unfolded state.
Kind Regards,
Thomas
On Thu, September 1, 2011 4:09 pm, KIRTANA S wrote:
> I want to calculate the free energy change while my polymer folds.
> I have used Implicit solvent, explicit solvent and also vacuum for my
> simulation .
>
> How can I get the energy of the complex only throughout the simulation
> run.
>
> Thanks in advance
> kirtana
>
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>
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Fri Sep 02 2011 - 00:00:02 PDT
