AMBER Archive (2008)

Subject: AMBER: Ptraj | Multiple trajout commands?

From: Ian (
Date: Fri May 30 2008 - 03:39:23 CDT

Hello All,

Is it possible to use multiple trajout commands to produce multiple output
trajectories in ptraj? I would like to input my trajectory once, but output
it at two different points during processing, e.g.:

trajin input.trj
strip :WAT
trajout output1.trj
strip :K+
trajout output2.trj

If I run this (ptraj v9.0), I just get "output2.trj" with *both* waters and
ions stripped out.

I found an old post (2006?) suggesting that it would be nice to have the
option of using multiple trajout commands. If it is already implemented, how
do I set it up? If not, I guess I just have to use multiple ptraj scripts ..

Many thanks,


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