AMBER Archive (2009)

Subject: Re: [AMBER] problem of mm_pbsa

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Wed Aug 05 2009 - 19:22:13 CDT

Dear Case,
Thanks very much for your suggestion of analysis by hand! But could you give me some clue about how to analyze by hand, or some of your experience? Thanks in advance!

Best wishes!

Qinghua Liao

________________________________
From: case <case_at_biomaps.rutgers.edu>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Wednesday, August 5, 2009 11:42:56 PM
Subject: Re: [AMBER] problem of mm_pbsa

On Tue, Aug 04, 2009, Qinghua Liao wrote:

> I have a problem when I use mm_pbsa in amber 10Â to calculate the
> binding energy of the complex. After docking using autodock 4.0, I chose
> a conformation of the ligand, which matched well with the crystal ligand
> in the complex, to do MD with the receptor, two structural waters were
> preserved. I got a sample of 4ns, a equilibrated system according to the
> RMSD of the backbone.
>
> But the binding energy is abnormal:
>
> #                  COMPLEX                RECEPTOR                  LIGAND       
> #          ----------------------- ----------------------- -----------------------
> #                  MEAN        STD         MEAN        STD         MEAN        STD
> #          ======================= ======================= =======================
> ELE            -8427.58     249.82     -7913.17     248.20      -504.26      14.77
> VDW         21573827.80   32502.03  20373193.05   31945..80   1200511.78    3894.24
> INT          7034641.54   60631.76   6982919.11   60080.98     51722.43    5624.52
> GAS         28600041.76   67739.75  27348198..98   66677.44   1251729.96    7136.00
> PBSUR            104.47       1.36       104.04       1.33         4.94       0.08

You will have to do the analysis (at least some of it) "by hand".  Look at the
output files from your simulation: why do you have such high van der Waals and
internal energies?

The MM-PBSA perl scripts are nice when everything works, but are much less
helpful when problems show up.  In such circumstances, you should at least a
part of the analysis yourself, so that you really understand what is being
computed.  Further, everyone's "first" analysis should also be done this way.

...good luck...dac

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