AMBER Archive (2009)

Subject: [AMBER] re: charge interaction

From: Jio M (jiomm_at_yahoo.com)
Date: Sun Sep 13 2009 - 09:38:43 CDT

Dear Amber users and Case;

Sorry for not able to make my query so much clear...I have changed some points.. if still not clear I will try to modify

I want to do mm_pbsa for protein drug
interaction. I docked my protein-drug
structure in flex x. I will make separate pdb for my drug
keeping same coordinates as in complex pdb obtained from docked results. For drug I can use
antechamber(gaff)

Docking needs charges to be assigned on each atom. but when we use xleap and
source the force field for protein all the atoms and charges are
assigned according to amino acid residues templates defined in
library....also the drug atom will get charges from antechamber..( according to the -c flag) this
will change the charges on each atom as were already there in docked result. coming
to my real query, while docking the interaction is made according to
the charges so assigned (by software itself) to the atoms i.e. the coordinates should change
if we change the charges because charges leads to interaction hence the spacial arrangement of the atoms

but it is the not the case we use the coordinates so generated while
docking but charges are used by sourcing force filed and hence
corresponding library residues charges already there in amber library structures so it should affect interaction energy
calculations in MMPBSA method also

Thanks and regards
JIomm

      
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