AMBER Archive (2009)

Subject: Re: [AMBER] Error in binding energy (MM PBSA)

From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Thu May 07 2009 - 06:33:20 CDT

On Thu, May 07, 2009, Vikas Sharma wrote:
>
> I am using Amber10..
> i used MM PBSA for binding free energy calculation...
> I used antechamber (AM1 BCC charges)...i performed a 1 ns simulation with 1 fs time step...
> after production MD i extracted the co-ordinates and then calculated free enrgy using MM PBSA...i am getting delta PBTOT as a positive value...

This doesn't sound like a problem that can be solved via email. You should
study the behavior of your system, look at individual snapshots, essentially
run the MM-PBSA calculation "by hand" to see if anything looks suspicious.
It looks like you may have a very big system, so you will have to be quite
careful to get everything right.

...dac

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