AMBER Archive (2008)

Subject: AMBER: ptraj and netcdf with AmberTools1.2 ?

From: Lars Skjærven (
Date: Mon Sep 01 2008 - 04:11:23 CDT

Hi there,

When updating from AmberTools 1.0 to 1.2 I discovered I could no
longer read my binary trajectory files. Double checking this shows
that compiling AT-1.0 ptraj works fine with respect to this, but
AT-1.2 results in "could not open file".

I use "./configure_at gcc" in both cases. I've tried this on two
separate machines, with the same result on both. It seems to me that
NetCDF compiles in both cases, and "make check" in
$AMBERHOME/src/netcdf/src works fine as well in both cases (for AT-1.0
and AT-1.2). Writing a binary trajectory file works on the other hand
just fine (with AT1.2).

Any clues ? Is it just me (or my settings), or is this a common problem?


Lars Skjaerven
University of Bergen, Norway
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