AMBER Archive (2009)

Subject: Re: [AMBER] problem of mm_pbsa

From: case (case_at_biomaps.rutgers.edu)
Date: Wed Aug 05 2009 - 10:42:56 CDT


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

> I have a problem when I use mm_pbsa in amber 10¬ 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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