Dear respected Jordan Monnet,
Thanks for your reply and suggestion! And also I am sorry for replying late. I have found what the problem really is.
The problem is because that I had kept two structural waters in the receptor, which were near the active sites. And I did something wrong when re-generating the topology files of ligand, receptor and complex, in which the number of atoms mismatched with the topology file of complex solvated with TIP3PBOX model generated before.
So I just want to ask you another question, when I want to keep some structural waters, how should I prepare the topology files of ligand, receptor, complex and solvated complex? And how to analyze the interactions involving these structural waters after simulation? Thanks very much in advance!
All the best,
Qinghua Liao
________________________________
From: Jordan Monnet <monnet..jordan.free.fr>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, August 11, 2009 3:37:55 AM
Subject: Re: [AMBER] problem of mm_pbsa
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
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
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> >
> >
> >
> >
> > _______________________________________________
> > 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 - 22:23:07 PDT
