On Sun, May 1, 2011 at 12:19 PM, Lekpa Duukori <duukori.gmail.com> wrote:
> Hi all,
>
> I want to use MMPBSA to study a trimer formation process, so what I have
> could be called a 'complex' and 'ligand'.
>
> What I want to do is:
>
> C - 3*L
>
For clarity, I will refer to the above as C - 3*M (M for monomer)
>
> Instead of the usual:
>
> C - ( L + R)
>
> I know I can do this manually but it would be great to use the MMPBSA
> machinery if there is a simple way I can do so.
>
Why not just make the definition R = 2*M, L = M. This gives the ultimate
result from MM/PBSA of C - (L + R) = C - (2*M + M) = C - 3*M, which is what
you're looking for, no?
You won't be able to determine each monomer's contribution (there's no way
to do *3* ligands, but you can get the total difference in the above way).
HTH,
Jason
> Any ideas?
>
> Many thanks,
>
> Lekpa
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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 Sun May 01 2011 - 04:00:03 PDT
