There seems to be a problem with the inputs being given to the PB solver.
The PB solver was not able to properly run, which is why no PB mdout file
created. Since the run failed, all temporary files must have been kept. Did
you check the ptraj output files to make sure the program stripped out the
proper residues and recognized the correct files? Were *any* mdout files
created? What was printed in the logfile (or to the screen if ran
interactively). If you submitted the run to a queue, what was printed in the
.out and .err files? Are you just running PB, or GB also?
-Bill Miller
On Mon, Mar 1, 2010 at 11:14 AM, Dwight McGee <dwight.mcgee.gmail.com>wrote:
> Hi Cristina,
>
>
> If you go to the amber manual look under the igb section you will see that
> each generalized born model rather it be 1,2,5,7 has a suggested pbradii.
> MMPBSA.py simply checks your topology files to see that the pbradii you
> specified matches up to the generalized born model you have chosen if they
> do not match to the suggested models then it prints the message which you
> observed.
> If you want to use igb=5, I would remake my topology and coordinate files
> adding the command
> *set default PBradii mbondi2* or *set default PBradii bondi*
> Hope that helps.
>
> Good Luck
>
>
> On Mon, Mar 1, 2010 at 11:04 AM, Cristina Sisu <csds2.cam.ac.uk> wrote:
>
> > Hi,
> >
> > Thank you both for the answers.
> > >> Before to do that you could try with the new MM_PBSA.py. I don't know
> > how it
> > >> works with Zinc, maybe it is more "user friendly" than the old MM_PBSA
> > perl
> > >>
> > >
> > > It takes the Zinc radius from the prmtop file. It does this because
> > > there is no option to use molsurf, which would require an external
> > > definition of the radius. However, results with/without molsurf
> > > differ only very slightly in my experience. I believe mm_pbsa.pl also
> > > has an option to do this, though I'm not familiar enough with using
> > > that version to speak definitively on it.
> > >
> > >
> > I've tried the MM_PBSA.py and it seems to recognize both Fe and Zn and
> > that's good, however I stumbled onto another problem. I set the
> > MM_PBSA.py running and shortly after checking the complex. receptor and
> > ligand file I get the error:
> >
> > > Assuming /usr/local/amber9/exe/sander is part of
> > > amber9 or amber10. Using old PB input file.
> > > Warning: igb=5 should be used with either mbondi2 or bondi pbradii
> > > set. Yours are modified Bondi radii (mbondi)
> > > Residue labels:
> > >
> > > Checking coordinates: ../JMJC-noalyprod-1.mdcrd
> > > Residue labels:
> > >
> > > Checking coordinates: _MMPBSA_complex.mdcrd
> > > Residue labels:
> > >
> > > Checking coordinates: _MMPBSA_complex.mdcrd
> > > Residue labels:
> > >
> > > Checking coordinates: _MMPBSA_complex.mdcrd
> > > Residue labels:
> > >
> > > Checking coordinates: _MMPBSA_receptor.mdcrd
> > > Residue labels:
> > >
> > > Checking coordinates: _MMPBSA_ligand.mdcrd
> > > Error: Sander error! PB mdout file was not created.
> > > ~
> > I've tried all the versions to run MM_PBSA.py in serial and parallel.
> > I've checked all the input parameters. Still I have no idea of what is
> > happening. There is not extra information except the error: "Sander
> > error! PB mdout file not created"
> > Any ideas as to what can be going so wrong here?
> >
> >
> > Cristina
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> T. Dwight McGee Jr.
> Quantum Theory Project
> University of Florida
> dwight.mcgee.gmail.com
>
> "Problems cannot be solved at the same level of awareness that created
> them."
> Albert Einstein
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 01 2010 - 08:30:04 PST
