Hello,
Can you send us one of your "something_com.all.out" from the run which gives
you these weird results?
--Jordan
* Qinghua Liao (fantasticqhl.yahoo.com) wrote:
> 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.gmail.com>
> To: AMBER Mailing List <amber.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.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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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}><(({*>
__/
Jordan MONNET
Bachelor in Biology & Computer science
University of Paris Diderot (Paris VII)
http://monnet.jordan.free.fr/
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Received on Wed Aug 19 2009 - 20:59:42 PDT
