Hi Thomas,
MMPBSA calculates the change in binding free energy of the ligand and receptor.
How can I use this only for the complex only.
Thanks
kirtana
Fri, Sep 2, 2011 at 2:43 AM, <steinbrt.rci.rutgers.edu> wrote:
> 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 - 11:00:04 PDT
