AMBER Archive (2009)

Subject: Re: [AMBER] combine many coord files into trajectory file

From: Carlos Simmerling (
Date: Tue Mar 31 2009 - 08:55:58 CDT

I don't think ptraj has any facility for reading a sereis files, Tom may
know. you can write a script to create the ptraj input though, just with
lots of trajin lines.
easioer may be your second request about reading each 10th frame. this is
easy, just add numbers to the trajin command for first, last and stride:

trajin mdcrd 1 100000 10

On Tue, Mar 31, 2009 at 9:51 AM, Peter Gannett <> wrote:

> All:
> I have a large number of coordinate files (1300+) that I want to combine
> into a trajectory. The files are number consecutively (e.g. file1.crd.0001,
> file2.crd.0002....file1300.crd.1300). How can I combine these files, in the
> proper order, into a trajectory? I know ptraj can do this just by reading
> in each and then dumping to a trajectory file but I don't know how to get
> ptraj to do this with just a single trajin coupled with some way to get it
> to step through the crd files.
> Alternately, is there a way to read in every 10th frame, for example, from
> a trajectory file?
> Thanks
> Pete Gannett
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