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AMBER Archive (2009)Subject: [AMBER] re: charge consideration
From: Jio M (jiomm_at_yahoo.com)
Dear Case;
Sir, I actually wanted to know what you replied :-)
>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
we can use "starting" coordinates and charges from other docking
thanks and regards:
Jiomm
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
>
> > 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.
^^^^^ "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.
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