Re: [AMBER] Ptraj crashes and Hbond analysis

From: Thomas Cheatham III <>
Date: Tue, 22 Mar 2011 17:33:37 -0600 (Mountain Daylight Time)

> 1) I'm experiencing a problem where I use ptraj scripts to analyze several
> simulations of structures very similar to each other. The scripts mostly
> work, but when I use this script for a certain few structures ptraj
> consistently crashes. Has anyone else experienced this?

There is insufficient information provided to comment.

> 2) Could someone please point me to one of the emails that explain the
> "time" keyword in the "hbond" command? I know there are several in-depth
> explanations of this facility in the archive, but I haven't been able to
> find them.

The trajectory file only contains coordinates; there is no information on
time or the interval of time between frames. Therefore this keyword
allows specifying the "time" interval between frames, in picoseconds. If
you have frames processed every 1 ps, "time 1.0" is appropriate. If every
100 ps, "time 100.0".


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Received on Tue Mar 22 2011 - 17:00:03 PDT
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