AMBER Archive (2009)

Subject: Re: [AMBER] problem of mm_pbsa

From: Jordan Monnet (monnet.jordan_at_free.fr)
Date: Fri Aug 07 2009 - 18:13:57 CDT


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_at_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_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 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
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
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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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