Hi everybody,
I´m studying the interaction between a series of ligands and a protein.
First i performed a docking study to choose the best molecules and proceed
later with a MD refinement.
With the docking program (ATD) i obtained a measure of the binding energy
(between -7 -8 kcal/mol), in the range of the experimental studies.
When later i use MMPBSA (once checked that the quality of the simulation
was rigth) i obtained a different scale of binding energies (between -2
and 0). No entropies were calculated.
Obviously, the codes of the programs will yield different results...
... but so large?
My question is either is common to obtain this kind of results (assuming
the overall process is right: quality of the simulation, stability,
correct split of the trajectory and prmtop files, setting up the
variables,...) in docking analysis followed by MD refinement and MMPBSA
calculation.
Thank you so much.
Carlos
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 27 2013 - 01:30:05 PDT
