Hi Amber users,
I read through the tutorial concerning binding energy calculations for the
wild type and alanine mutant (alanine scanning). What I understand from the
tutorial is that the mdcrd file is needed only for the wild but not for the
mutant (which means we do not need to run MD simulation for the mutant), am
I right???
My second question is, if I run two independent MD runs for the wild and the
alanine mutant, then calculate the PBSA binding energies for these two
systems independently, will that give me more accurate estimate about the
contribution of alanine to the binding than the scanning procedure does?
Best wishes
Mahmoud
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Received on Fri Apr 01 2011 - 13:30:03 PDT
