Re: [AMBER-Developers] Auto-image code in Cpptraj

From: Jodi Ann Hadden <>
Date: Fri, 8 Jun 2012 21:08:46 +0000

I had a particularly bad imaging nightmare I needed to work with today, so thought I'd give this new command a shot... This is a protein-carbohydrate complex solvated with a truncated octahedron. I used iwrap and did not save waters. The files came out of the MD imaged really weird, like the solvent and solute are imaged to different origins or something, and the ligand ends up wrapped into the other side of the cell. I have managed to image this system before, but it was not straightforward and took a while to find just the right magic combination of ptraj commands to do it...

With autoimage it just works! Amazing! Thanks Dan! :-)

I will note that since this system did require some "unwrapping" functionality and the trajectory did not contain waters, I had to provide a prmtop without waters but which had octahedral box information in order to unwrap my ligand to the correct place and get it back into its binding site. I've seen this confuse people before when using the unwrap command on a trajectory with no waters, the need for box information in the topology file... While this is intuitive, I just think this should be noted in the command documentation for the sake of n00bs.

The blessings of Glycon on you Dan! You've prevented many a graduate student tear with this improved functionality! :-)

On Jun 6, 2012, at 6:16 PM, Daniel Roe wrote:

> Hi All,
> I've implemented a new command in GIT/master cpptraj named
> 'autoimage'. The intent is to take most of the frustration out of
> imaging and have it just "work". An example of the usage is:
> parm test.parm7
> trajin
> autoimage
> trajout
> Note also that 'trajout' will now automatically determine output traj
> format via filename extension if no keyword is given (in this example
> netcdf traj). Recognized extensions are .nc, .ncrst, .pdb, .mol2,
> .dcd, .rst7, .crd.
> I have tested the code on a trajectory with split-up DNA molecules and
> it put them back together nicely. If anyone has any problematic
> trajectories (especially things like tetramers etc) and would like to
> give it a try I'd be interested to hear if it worked for you or not.
> Alternatively, if anyone would like to provide me with the
> topology/trajectory to test myself that would be appreciated as well.
> -Dan
> --
> -------------------------
> Daniel R. Roe, PhD
> Lab Specialist
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> (801) 587-9652
> (801) 585-9119 (Fax)
> _______________________________________________
> AMBER-Developers mailing list

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Received on Fri Jun 08 2012 - 14:30:03 PDT
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