AMBER Archive (2009)

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

From: David Watson (
Date: Mon Nov 09 2009 - 13:28:31 CST

On Nov 9, 2009, at 1:14 PM, Wallace Kunin wrote:

> Hello all, I am trying to install AmberTools 1.2 on Ubuntu 9.10
> (Karmic
> Koala). I have read through many posts about installing ambertools
> on
> ubuntu but none of the methods described have been totally
> successful. It
> appears that I am having issues with compiling some of the fortran
> code. I
> have every x11 package available and every fortran package
> available. I
> also downloaded g77 3.4 and its associated packages from the Ubuntu
> Hardy
> 8.04 (Hardy Herron) archive so that I have both gfortran and g77. I
> also
> have f2c, fort77, csh, g95 and the other current gcc compilers.
> 1. Ubuntu uses /usr/lib as the location of its x11 libraries not
> user/X11R6/lib. Does this affect my installation? I have edited the
> directories in which configure_at searches for the x11 libraries so
> that it
> does not give the error that the x11 libraries are not in the usual
> place.
> xLeap compiles fine if I use gfortran.
> 2. It seems that with gfortran, my compilation errors out in
> installing
> gleap but with g77 I get a bunch of gfortran commands that it can't
> read.
> Below are two makefile outputs. The first is with g77. The second
> is with
> gfortran. Also, could the option flags on either compiler that I
> set affect
> things? I have kept these the default used in the configure_at file.

For your G77 run, you obviously have not configured ambertools
properly, because it is including symbols for gfortran.
It should die somewhere in the process of compilation, when running

As for the gfortran run, it is apparently running properly, but...
before you rerun your make -f Makefile_at, you need to:
     make -f Makefile_at clean

In fact, should you desire to change compilers and try again, you
should always perform this "clean"-ing.

AMBER mailing list