AMBER Archive (2009)

Subject: [AMBER] charge consideration

From: Jio M (jiomm_at_yahoo.com)
Date: Fri Sep 11 2009 - 15:17:34 CDT

Dear Amber users;

I want to do mm_pbsa according the tutorial, but for protein drug
interaction. I have a general question.I have my docked protein drug
structure. as given in tutorial I will make separate pdb for my drug
keeping  same coordinates as in complex pdb. for drug I will use
antechamber(gaff)

While docking some charges were assigned . but when we use xleap and
source the force field for protein all the atoms and charges are
assigned according  amino acid residues templates defined in
library....also the drug atom will get cahrges from antechamber.. this
will change the charges as were already so assigned in docking. coming
to my real query, while docking the interaction is made according to
the charges so assigned to the atoms i.e. the coordinates should change
if we change the charges.

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.. so it should affect interaction enrgy
calculations also

Thanks and regards

JIomm

      
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