Re: [AMBER] :Re: "closest" command in cpptraj

From: Thomas Evangelidis <>
Date: Tue, 17 Apr 2012 17:29:51 +0300

I apologize for the shameful plug, but in case you could convert your
trajectory to .psf/.dcd then you could use "Truncate Trajectory" VMD plugin:

Only an alpha version is available at the moment, which cannot keep the
closest waters around the ligand (because it is a hetero atom) but a
possible workaround would be to keep the closest N waters from a protein
atom(s) that is very close to the ligand. Of course the ligand will be also
included in the output trajectory. The advantage of this plugin is that it
runs in parallel and it is really fast.

good luck,

On 17 April 2012 16:14, Daniel Roe <> wrote:

> Hi,
> On Tue, Apr 17, 2012 at 8:44 AM, Alfredo Quevedo
> <> wrote:
> > The point is that the calculation of distances is
> > rather slow, that is why I wanted to run it in parallel using cpptraj.
> > Unfortunately I find that the "closestwater" command is not included in
> > cpptraj.
> I'm confused by this. The 'closest' command is the same as the
> 'closestwater' command. In ptraj 'closestwater' was just the longer
> name for the shorter alias 'closest'. So in that sense 'closestwater'
> is in cpptraj, just now it is called 'closest'. In addition, this
> command is one of the actions in cpptraj that is OpenMP parallelized;
> let me know if you have problems compiling with OpenMP or getting the
> OpenMP version of cpptraj to work correctly.
> -Dan
> _______________________________________________
> AMBER mailing list

Thomas Evangelidis
PhD student
Biomedical Research Foundation, Academy of Athens
4 Soranou Ephessiou , 115 27 Athens, Greece

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Received on Tue Apr 17 2012 - 08:00:03 PDT
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