AMBER Archive (2008)

Subject: AMBER: MM-PBSA multiple trajectory problem

From: Carra, Claudio (JSC-SK)[USRA] (Claudio.Carra-1_at_nasa.gov)
Date: Wed Aug 27 2008 - 09:16:38 CDT

Dear All,

I've been trying to calculate the binding free energy with MM-BPSA using
the mm_pbsa.pl script

implemented in amber 10. For the single trajectory all looks fine, the
binding energy looks

reasonable, however, for a multiple trajectory I've encountered a
strange problem.

I've run separately the MD for the ligand and receptor, and calculate
the MM-PBSA energies

in three different cases by considering the complex, the ligand, and
receptor only as a receptor,

accordingly to the method we have to follow.

The ligand and the complex gives similar energy components to the one
calculated for the single

trajectory case, however, the receptor has a very different values,
except for the Eint which is very

similar to the single traj case, that should indicate the geometry is ok
(all the STDs look fine too).

I've check few times and all seems consistent, the method the parameters
and the ff used.

I've tried two different systems and I got the same problem, even if I
use amber 9.

I would really appreciate if someone could point me to where a potential
error might be.

I'm sure I'm missing something.

thanks a lot

sincerely

claudio

 

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