AMBER Archive (2009)

Subject: [AMBER] re: charge consideration

From: Jio M (jiomm_at_yahoo.com)
Date: Mon Sep 14 2009 - 03:38:27 CDT

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
programe..it was confusing me that whether we can use starting
coordinates and charges from other programe or not and then do dynamics
and mm_pbsa calculations giving AMBER charges

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

>
> 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.

      
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