Dear,
Greetings.
Lately I want to calculate entropy of some protein-ligand system. As known,
it is very memory-demanding if one uses mm_pbsa script. Therefore I want to
use nmode to calculate the entropy. By setting ismem as 1, I hope to reduce
the memory size to 1/3 as said in the manual. Since this is my first time
to use nmode, three questions are in my mind:
(1) the results of nmode are the same as those produced
by mmpbsa_py_nabnmode?
(2) since in nabnmode the maxcyc is set as 10000, should I set maxcyc as
10000 in nmode?
(3) As mentioned, the entropy I got is for the complex. if at the same time
I want to get the according entropy for the protein and the ligand, what
should i do? Extract the trajectory and then separate them into protein and
ligand? If so, after I minimized them, the structure must deviate from
those in the complex. In this situation, is the entropy data still reliable?
Suggestions from anyone would be greatly appreciated.
Rgds,
C.Q.Yan
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Received on Mon Aug 05 2013 - 02:00:02 PDT
