Dear all,
In the calculation of binding free energy between protein-ligand, if I want to know the interaction energy between ligand and the residues within a specific distance around it, how should I set the parameters in the input files? According to the instructions in manual, the 'idecomp' parameter will seem to give every pairwise interaction energy between residues in the studied system. This will cost a lot of computational time to the large system. Would you like to give me some suggestions about interaction energy calculation only considering ligand and its neighbor residues? Thank you!
Best wishes,
Duan Baogen
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Received on Sat Dec 08 2012 - 22:30:03 PST
