Hello,
I was wondering whether you had a couple of "wrong" snapshots which would
screw up the statistics. But ALL of your calculations give that very
high VDW energy! As already said, you want to re-check everything
carefully...
It could be a problem while reading your trajectory, you want to re-check
NTOTAL, LSTART, LSTOP etc. and be sure it does what you want it to. Is
your system solvated? If yes, I would try to strip water and ions using
ptraj and do the mmpbsa to see if it still wrong.
Good luck!
--jordan
* Qinghua Liao (fantasticqhl.yahoo.com) wrote:
> Hi Jordan Monnet,
>
> Thanks for your interest in this problem! The attached files are what you ask me to attach. Thanks!
>
> Best wishes!
>
> Qinghua Liao
>
>
> ________________________________
> From: Jordan Monnet <monnet.jordan.free.fr>
> To: AMBER Mailing List <amber.ambermd.org>
> Sent: Saturday, August 8, 2009 7:13:57 AM
> Subject: Re: [AMBER] problem of mm_pbsa
>
> 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
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> }><(({*>
> __/
>
> Jordan MONNET
> Bachelor in Biology & Computer science
> University of Paris Diderot (Paris VII)
>
> http://monnet.jordan.free.fr/
>
> _______________________________________________
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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 - 21:19:38 PDT
