Thank you so much Jason.
On 05/03/2014 10:08, Jason Swails wrote:
> 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
>
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Received on Fri Mar 07 2014 - 00:00:02 PST
