You can define "receptor" and "ligand" to be whatever parts of the system
that you want. If you have 2 physical ligands in your system (let's say L1
and L2), you can designate the following:
'receptor' == R + L1, 'ligand' == L2
'receptor' == R + L2, 'ligand' == L1
'receptor' == R, 'ligand' == L1 + L2
Each gives a different 'delta G'.
HTH,
Jason
On Tue, Nov 27, 2012 at 12:05 PM, Shuyi Cao <scao4.uic.edu> wrote:
> Hi, all
>
> In my PDB file, there are more one ligand in the system. Is it possible to
> calculate the binding free energy of those ligands as a whole using MMPBSA?
>
> Thank you in advance for any help!
>
> --
> Shuyi Cao
> Graduate student
> Department of Medicinal Chemistry and Pharmacognosy
> College of Pharmacy
> University of Illinois at Chicago
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Nov 27 2012 - 10:00:02 PST
