AMBER Archive (2006)

Subject: Re: AMBER: Problem with ptraj

From: Thomas Cheatham (
Date: Tue Sep 12 2006 - 21:47:46 CDT

> I am trying to use ptraj to analyse hydrogen bonds. but

To provide more input about your atom selections, set

  prnlev 3

> acceptor T N3 H3

...before the donor/acceptor commands...

> {\rtf1\ansi\ansicpg1252\deff0\deflang1033{\fonttbl{\f0\fswiss{\*\generator
> Msftedit;}\viewkind4\uc1\pard\f0WARNING in ptraj(): No input
> trajectories specified (trajin), aborting...

I do not understand all that extra font information (probably from your
e-mail program), but basically ptraj cannot find the trajectories in your
current directory.

> I have checked that the input file DNA_melt.mdcrd is in the $AMBERHOME
> directory.

The file should be in your current directory, not in $AMBERHOME, unless of
course you are running ptraj from $AMBERHOME.

Good luck,

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