AMBER Archive (2009)

Subject: Re: [AMBER] re: charge interaction

From: case (case_at_biomaps.rutgers.edu)
Date: Sun Sep 13 2009 - 16:37:55 CDT

On Sun, Sep 13, 2009, case wrote:

> 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
                                                                  ^^^^^^^^^
                                                                   "compute"

> energies, again using the Amber charges. So the charges and the coordinates
> would be consistent with each.
                           ^^^^^ "each other."

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

sorry for the typos...I should proofread more carefully....dac

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