AMBER Archive (2009)

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

From: Peter Gannett (
Date: Tue Mar 31 2009 - 08:51:16 CDT

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?
Pete Gannett
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