Are you doing a pairwise decomposition (idecomp=3,4) or a pairwise
decomposition (idecomp=1,2)? Your subject would suggest the former.
The ligand will probably undergo the largest SASA change, since it goes from
"buried" to completely solvent-exposed, so its non-polar solvation term will
be the largest of any residue in the system.
However, without knowing more details about what exactly you're doing, I
can't provide much more explanation (i.e. are you using MM/PBSA, either
MMPBSA.py or mm_pbsa.pl, or just manually setting idecomp in the sander mdin
file, etc.)
All the best,
Jason
2010/5/27 Catein Catherine <askamber23.hotmail.com>
>
> Dear Sir/Madam,
>
>
>
> I have done a GBSA calculation for a drug-protein complex. I found the a
> list of energies for each residues in the complexes with drug.
>
>
>
> I could understand the meaning of protein residue-drug energies phyiscally.
>
>
>
> However, I found the energies for drug-drug is highest among all the
> residues in the complex. Why? What is the physical meaning of drug-drug
> interaction?
>
>
>
> Best regards,
>
>
>
> Cat
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu May 27 2010 - 07:00:05 PDT
