Re: [AMBER] ptraj: Sort trajectory based on protein-ligand distance

From: g t <>
Date: Wed, 14 Mar 2012 18:37:31 +0000

use distance command to output distance between a point on your ligand and
a point on your protein. this should output a file with frame number and
distance columns.

write a script (e.g. python) that selects the frames that have a distance
under 15 A. then feed this into ptraj so it writes out a new co-ordinate
file with only those frames.

not sure what you meant by the pdb bit at the end of your message. did you
mean crd?


On 14 March 2012 01:27, <> wrote:

> Hello,
> I try to use ptraj/cpptraj to sort my trajectory based on the
> protein-ligand distance. I want to remove all of the snapshots in which
> the distance between protein and ligand is greater than 15 angstroms and
> store the rest of the trajectory into one PDB. Please give me some
> suggestions.
> Thanks,
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Received on Wed Mar 14 2012 - 12:00:02 PDT
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