I have checked strip_mask and I saw that Mg atom was in the list. After removing it from list the results are acceptable now. Thank you Mr. Swails and Mr. Case.
________________________________
From: Jason Swails <jason.swails.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sunday, February 5, 2012 8:08 PM
Subject: Re: [AMBER] mmpbsa
Also try visualizing the trajectories that were generated by MMPBSA.py with
the corresponding topology files. My guess is that they will look very
warped.
Common things that can happen and to look out for: look at strip_mask
(particularly the default value listed in the manual). Do you have ions
(or anything else) that you _expect_ to be stripped out that are not
specified by that strip_mask? If so, you will have to specify a strip_mask
to properly remove them. Do you have any waters or ions or anything else
in your complex topology file that is included in strip_mask? If so, then
this molecule is being stripped out of the trajectories, which can lead to
these errors. You'll have to redefine strip_mask to omit the residues that
you want to keep.
The topology files themselves appear to be OK since the default mask
guesser didn't complain about anything (in this version, as long as
MMPBSA.py properly guesses the receptor and ligand masks, it will also
check for charge consistency -- the next version will check for charge
consistency in every case).
Another thing you can check is to set "netcdf=1" in the &general section --
this will generate NetCDF intermediate trajectories which have more
information than their ASCII counterparts (including the number of atoms
present in the trajectory). This provides another layer of error checking.
This way, you'll be able to see exactly how many extra (or how many fewer)
atoms your trajectory has compared to your topologies (ncdump is a useful
utility to look at the contents of a NetCDF file).
HTH,
Jason
On Sun, Feb 5, 2012 at 12:44 PM, case <case.biomaps.rutgers.edu> wrote:
> On Sat, Feb 04, 2012, Sel Ercan wrote:
>
> > Can anyone tell me why the values obtained from MMPBSA are so large? I
> > also run mm_pbsa.pl and its results were plausible.
> >
> > WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL TERMS (BOND,
> > ANGLE, AND/OR DIHED).
> > CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS
> > MAY NOT BE RELIABLE (check differences)!
> >
> >
> > WARNING: INCONSISTENCIES EXIST WITHIN 1-4 NON-BONDED TERMS.
> > CHECK YOUR INPUT FILES AND SYSTEM SETUP. THESE RESULTS
> > MAY NOT BE RELIABLE (check differences)!
> >
>
> Something is very wrong with your topology files or setup. But there is
> not
> enough information given for us to figure out what. You should examine the
> individual output files to look for clues.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Feb 05 2012 - 13:30:02 PST
