MMPBSA.py(.MPI) will remove the chloride ions from the trajectory
automatically unless strip_mdcrd=0 (strip_mdcrd=1 is default).
MMPBSA.py(.MPI) will remove all water molecules and all ions from the
trajectory by default. Are there any ions in your prmtop files? This error
is almost certainly due to an incompatibility between the prmtops provided
and the trajectory files made and used by MMPBSA.py.MPI. Do you intend to
keep the ions for the calculation or not? You can control what ions and
molecules are stripped from the trajectory file by MMPBSA.py(.MPI) by
changing the strip_mdcrd and strip_mask variables. See the manual for more
info.
Good luck!
-Bill
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
> 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')
>
> 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
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Mon Dec 06 2010 - 21:00:03 PST
