AMBER Archive (2009)

Subject: Re: [AMBER] problem of mm_pbsa

From: Qinghua Liao (fantasticqhl_at_yahoo.com)
Date: Thu Aug 06 2009 - 18:58:55 CDT

Hi sir,
Many thanks for your reply! I have done that too, but there is no problem. I am wondering that maybe the two structural waters will make a difference, so I am just doing another simulation without the two structural waters. Thanks!

Best wishes!

Qinghua Liao

________________________________
From: Rubben Torella <rubben.torella_at_gmail.com>
To: AMBER Mailing List <amber_at_ambermd.org>
Sent: Thursday, August 6, 2009 11:53:47 PM
Subject: Re: [AMBER] problem of mm_pbsa

Hi,
try to check the structures of the ligand, repector and complex you created
for the analysis...
use the ambpdb command and check if every structure is correct...
Hope this could help...

2009/8/5 case <case_at_biomaps.rutgers.edu>

> 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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