Dear Amber developers,
I'm calculating by MM-PBSA the binding free energy values of two
enantiomers interacting with the same protein adopting similar binding
modes.
I performed the calculations by single-trajectory approach and the
obtained energy terms (Emm, Pbtot, pbsur, TSrot, TStras) for the two
enantiomers were essentially similar.
The only difference resides in the TSvib terms, in fact for the R
enantiomer I obtained 8.67 while for the S was 0.63.
Both enantiomers have similar nM affinity but the calculated DGbind was
very dissimilar.
Would one of the developers be so kind to explain this result?
It could be a problem of the binding mode supposed for the S enantiomer?
Thank you very much in advance,
G Grazioso
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Received on Tue Jan 12 2010 - 07:30:02 PST
