Re: [AMBER] [] Two questions (autoimage and parsing of output)

From: Eiros Zamora, Juan <>
Date: Fri, 3 Feb 2017 16:11:01 +0000

Hi Jason,

The trajectories are already imaged as I want them to be — using as anchor the protein, and not the ligand (and with the solvent stripped (:WAT) but not the counterions (:Na+,Cl-)). But after MMPBSA, the output trajectories have the ligand as the anchor of the autoimage command.

Also, do you know if each of the processors in the MPI version process the frames in serial? Or do they work with frames alternately?

Best regards,

> On 3 Feb 2017, at 13:06, Jason Swails <> wrote:
>> On Feb 2, 2017, at 9:52 AM, Daniel Roe <> wrote:
>> Hi,
>> It does appear that 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 - 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
> HTH,
> Jason
> --
> Jason M. Swails
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Received on Fri Feb 03 2017 - 08:30:02 PST
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