On Tue, Mar 4, 2014 at 8:56 PM, Maryam Azimzadeh Irani <
maryamai.bii.a-star.edu.sg> wrote:
> Dear Amber users,
> I am trying to run alanine scanning with with MMPBSA.py but I am getting
> this error for my mutated protein:
> WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL POTENTIAL
> TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE
> and all of the energy outputs are so huge in comparison to the normal
> MMPBSA for the same trajectory. I couldn't figure out whats the problem,
> would you help me with that?
>
Most likely your topology files are inconsistent with your trajectories.
The usual advice applies here: visualize your system and all of the
trajectory-topology pairings that MM/PBSA is using (for instance, visualize
_MMPBSA_complex.mdcrd.0 with your complex topology file,
_MMPBSA_receptor.mdcrd.0 with your receptor topology file, etc.). See if
you can figure out what step might be causing the inconsistency and why
they might be caused (is the default strip_mask stripping out a water or
ion that you intended to keep in your complex?)
Also look at the generated mutant trajectories to make sure that they are
consistent with your mutant topology files.
Finally, make sure you are using the latest version of AmberTools 13 with
all updates applied when running your calculations.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Mar 04 2014 - 18:30:03 PST
