Re: [AMBER] Selecting specific set of molecules for output trajectory

From: David A Case <>
Date: Tue, 9 Oct 2018 08:20:53 -0400

On Tue, Oct 09, 2018, anu chandra wrote:

> I wonder if there is way to filter the molecules to be selected while
> writing the output trajectory (i.e., with ntwx). I am aware of the 'ntwprt'
> to select a set of atoms while writing the trajectories. I wish to select
> specific molecules rather than 1 to ntwprt atoms. For e.g. I would like to
> keep 'proteins, and 'water' and leave the 'ligand' in between while writing
> the trajectories.

I don't think there is any way to do this during the MD run. After the
fact, you can use the "strip" command in cpptraj to select just what you
want, write out a new trajectory file (and corresponding new prmtop
file). Then you can delete the original trajectory file if you wish.


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Received on Tue Oct 09 2018 - 05:30:02 PDT
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