AMBER Archive (2009)

Subject: Re: [AMBER] problem of mm_pbsa

From: Jordan Monnet (monnet.jordan_at_free.fr)
Date: Thu Aug 13 2009 - 15:04:37 CDT


Hello,

I am not sure to understand what you want to calculate while keeping
these water molecules, perhaps someone else will be more helpful :)

To get an idea of what is going on with the water, you probably want to
use ptraj. see "grid" and "hbond" command

Good luck!

--jordan

* Qinghua Liao (fantasticqhl_at_yahoo.com) wrote:
> 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_at_free.fr>
> To: AMBER Mailing List <amber_at_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_at_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_at_free.fr>
> > To: AMBER Mailing List <amber_at_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_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
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > >†
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER_at_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/
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
>
>
>
>
>
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_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/
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_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/

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