AMBER Archive (2009)

Subject: Re: [AMBER] re: charge interaction

From: case (
Date: Sun Sep 13 2009 - 16:13:19 CDT

On Sun, Sep 13, 2009, Jio M wrote:

> ....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

It sounds like you don't understand what happens in the mm-pbsa method(?).
You might use the docked configuration from some other program as a starting
point, but then you would run a molecular dynamics simulation using the Amber
charges. From this simulation, you would extract snapshots, and computer
energies, again using the Amber charges. So the charges and the coordinates
would be consistent with each.

Note that mm-pbsa is never done with just a single set of coordinates (as from
the output of a typical docking program.


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