Re: [AMBER] problem of mm_pbsa

From: case <case.biomaps.rutgers.edu>
Date: Wed, 5 Aug 2009 16:42:56 +0100

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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Received on Wed Aug 19 2009 - 20:33:20 PDT
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