Fixed it, commented out line 633 of MMPBSA_mods make_trajs.py file and recompiled. Now it’s not autoimaging the trajectories.
I’ll try to see if I can figure out how the user can pass arguments to the ‘autoimage’ command through the mmpbsa.in file, if that’s a useful addition?
Best regards,
Juan
> On 6 Feb 2017, at 12:16, Eiros Zamora, Juan <j.eiros-zamora14.imperial.ac.uk> wrote:
>
> Dear Jason,
>
> If I’ve already autoimaged the trajectories properly, is there a way I can tell MMPBSA.py.MPI to not use the autoimage call? Maybe I could comment out the call in the source code of my installation, if you could point to me where it’s happening.
>
> Best regards,
> Juan
>> On 3 Feb 2017, at 13:06, Jason Swails <jason.swails.gmail.com> wrote:
>>
>>
>>
>>> On Feb 2, 2017, at 9:52 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>>>
>>> Hi,
>>>
>>> It does appear that mmpbsa.py makes use of the "autoimage" feature,
>>> and imaging can certainly affect your energies if the distances used
>>> are not properly imaged. I don't know if there is a way to pass
>>> 'autoimage' arguments to mmpbsa.py - hopefully one of the devs can
>>> comment on this.
>>
>> There is no way to do this. If you need different imaging, you will need to prepare the trajectory (and strip solvent) yourself before passing the files to MMPBSA.py
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
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Received on Mon Feb 06 2017 - 07:00:02 PST
