Dear Dr. Jason, Dr. Bill,
Thank you for your support. I will look for possible incompatibilities and
try to correct them.
Thank you
Regards,
kamlesh
On Wed, Dec 8, 2010 at 4:15 AM, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> Bill's email is completely correct, I just wanted to point out a potential
> flaw in something you may be assuming. See below:
>
> On Mon, Dec 6, 2010 at 11:21 PM, kamlesh sahu <kamleshsemail.gmail.com
> >wrote:
>
> > Hello amber users,
> >
> > I am running MMPBSA.py.MPI on trajectories obtained from MD simulation on
> a
> > complex which contained four ZN ions and two Cl- ions. I did not remove
> Cl-
> > before simulations. Can that be the reason why I am getting this error ?
> -
> >
> >
> >
> > Starting pb calculation...
> >
> > calculating ligand contribution...
> > calculating receptor contribution...
> > calculating complex contribution...
> >
> > Calculations complete. Writing output file(s)...
> > Error: Sander output is missing values!
> > VDWAALS = ************* EEL = -19824.2815 EPB =
> > -4539.5565
> > NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> > --clean to erase these files.
> >
> >
> >
> > The output file has correct guess for ligand and receptor so I guess the
> > prmtop and trajectories are compatible. Could you please tell me how to
> >
>
> The fact that the guess for the ligand and receptor are correct ONLY means
> that the ligand, receptor, and complex topology files are consistent with
> one another. That says nothing at all about whether or not they're
> compatible with your trajectories. I would bet that if you visualize your
> _MMPBSA_receptor.mdcrd file with your receptor prmtop (and the same with
> your complex and ligand prmtops), you'll see that they're not actually
> consistent.
>
> remove these Cl- ions from the trajectories before running MMPBSA.py (if
> Cl-
> > ions are the problem). I just did pb calculations (not gb because it was
> > saying 'bad atom type ZN')
> >
>
> You should probably remove ions unless they're explicitly part of binding,
> since implicit solvent accounts for the salt effects via a debye screening
> parameter (set via the variable "saltcon" in the MMPBSA.py input file). GB
> is not meant to deal with explicit ions.
>
> Also keep in mind that if you left the Cl- ions in your prmtop and wish to
> strip them, then you'll have to create new prmtop files to be consistent
> with the created trajectories.
>
> Good luck!
> Jason
>
>
> >
> > Thank you
> > kamlesh
> > --
> > Kamlesh Kumar Sahu (post doc researcher)
> > Riken, wako, Saitama, JAPAN
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Kamlesh Kumar Sahu (post doc researcher)
Riken, wako, Saitama, JAPAN
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Received on Tue Dec 07 2010 - 21:30:05 PST
