AMBER Archive (2004)

Subject: AMBER: mmpbsa: can not generate coordinates/snapshots

From: Magne Olufsen (
Date: Mon Sep 13 2004 - 05:37:54 CDT


I am trying to use mmpbsa to calculate protein stability, but the number of
coordinates written out by the mmpbsa script is not correct. I am using the
script as provided in the Examples. The number of coordinates in the .crd
file is 50, and this is also the number of coordinates found by carnal. If
I try to write out all files, only 38 out of the 50 is generated (with
start 1, end 50 and skip 1). There is not any understandable error message,
and the only complaint I get is:

Warning: no access to tty (Bad file number).
Thus no job control in this shell.

The examples also work out just fine, so we are having some difficulties in
understanding what might be wrong.
We are currently using Amber7, and the .crd file was generated by Amber6
but since the file format has not changed that should not make the problem.

Does anyone have any idea of what might be wrong?

        Magne Olufsen

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