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
