Dear amber users,
I am trying to compute binding energy of ligand covalently bound in hexa
coordinated heme protein. (Fe attached to 4 porphyrin N, 1 bonded with
proximal His and 1 with ligand). Successfully performed 10ns long
simulation of heme protein bound to ligand, and want to post process them
with mm_pbsa.pl script.
*How to use mm_pbsa.pl <
http://mm_pbsa.pl/> script to post process the
obtained simulation ?*
10ns simulation of complex -> give parameters files of complex
(Fe-hexavalent), ligand and protein (Fe-pentavalent) -> binding energy of
complex.
As per trials runs, i am getting broken structures (bcoz of hexa and penta
valent Fe, i suppose) and so wrong energies for my system.
Adding atoms gives mismatch in the total number of atoms.
Any help in this regard is highly appreciated.
Many thanks
Smriti
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Received on Tue Sep 06 2016 - 22:30:03 PDT
