AMBER Archive (2009)

Subject: Re: [AMBER] AmberTools 1.2 Installation on Ubuntu 9.10 Karmic Koala

From: Giorgio Maccari (
Date: Wed Nov 11 2009 - 10:53:04 CST


I think that the problem that you have found could be due to some
difference of the "sh" shell between ubuntu and RedHat based
distributions: in Ubuntu /bin/sh is a link to /bin/dash while in RedHat
is a link to /bin/bash. There are few differences between bash and dash,
but they are enough to raise some problems.

In your case antechamber call $AMBERHOME/exe/ and is this that
fail. One solution is to change the header of all the shell scripts in
the $AMBERHOME/exe folder from "#!/bin/sh" to "#!/bin/bash" (with out
quotation marks). You could type into a shell:

sed -i -s 's|#!/bin/sh|#!/bin/bash|g' $AMBERHOME/exe/*

This command will change all the headers and fix the problem.

My best regards.
Giorgio Maccari.

Il giorno mer, 11/11/2009 alle 09.17 -0500, Wallace Kunin ha scritto:
> This is the code from in the antechamber test folder.
> #!/bin/csh -f
> # "The Mulliken charges were generated by mopac in amber10;
> # you may get different result if different QM program is applied"
> ../../../exe/antechamber -i tp.pdb -fi pdb -o tp.mol2 -fo mol2 \
> -c bcc >& antechamber.out || goto error
> ../../../exe/parmchk -i tp.mol2 -f mol2 -o frcmod || goto error
> # ../../../exe/tleap -s -f > leap.out
> ../../dacdif -r 1.e-3 tp.mol2
> ../../dacdif frcmod
> # ../../dacdif -t 2 prmtop
> prmcrd divcon.rst divcon.dmx leap.log leap.out
> exit(0)
> error:
> echo " ${0}: Program error"
> exit(1)
> _______________________________________________
> AMBER mailing list

AMBER mailing list