AMBER Archive (2008)

Subject: Re: AMBER: Ptraj | Multiple trajout commands?

From: Jianyin Shao (
Date: Sat May 31 2008 - 19:02:17 CDT

Hi, Ian,

I think that ptraj run trajout command only once after all processing
command. You need to use two separate scripts to generate two trajout files.
If you have a lot of common commands for coordinate manipulation, you can
combine the common commands in a first script. I would not concern this too
much because coordinate manipulations usually don't take much time and

trajin input.trj
trajout output0.trj

 trajin input0.trj
strip :WAT
trajout output1.trj

trajin output0.trj
strip :K+
trajout output2.trj



On 5/30/08, Ian <> wrote:
> 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,
> Ian.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)