Re: [AMBER] error when running tleap from script, works fine from shell

From: David A Case <>
Date: Wed, 13 Dec 2017 09:14:30 -0500

On Tue, Dec 12, 2017, Andreas Tosstorff wrote:
> I am having a problem when running the following tleap command from a
> bash script:
> /tleap -f leapCys.script  >> Molecule.tleap.err
> Molecule.tleap.err then reads:
> /    Could not open file leaprc.parmbsc0_chiOL4_ezOL1: not found/

What else does Molecule.tleap.err say? Can you post the entire output, or the
entire output up to the error message listed above?

> Now when I run exactly the same command from the shell, I don't get any
> error, it works just fine:
> /tleap -f leapCys.script  >> Molecule.tleap.err/

Use a different output filename here, such as Molecule.tleap.good. Then
compare the good and bad files...that might provide some clues.

Also, do indeed check your PATHS: you might get the behavior you report if the
bash script was running AmberTools16 and the interactive command was running
tleap from an earlier version of AmberTools: leaprc.parmbsc0_chiOL4_ezOL1
is now in the oldff directory that contains obsolete force fields that are
only recommended for backwards compatibility or to continue old simulations.


AMBER mailing list
Received on Wed Dec 13 2017 - 06:30:03 PST
Custom Search