Re: [AMBER-Developers] Intel and At1.5/Amber11 combo (on rhel 4)

From: Jason Swails <>
Date: Thu, 9 Jun 2011 08:00:46 -0600

On Thu, Jun 9, 2011 at 4:35 AM, David A. Case <>wrote:

> On Wed, Jun 08, 2011, B. Lachele Foley wrote:
> > "Basically, each time you re-run configure, you also need to re-run the
> python script."
> >
> > Ahhh.... Between serial and parallel, I thought "hmmmm..... I wonder if
> running the python thing again will be necessary.... or if doing that will
> break things even worse... hmmmmm....."
> >
> > I chose not to. Works now. Thanks!
> >
> > I suppose the only way to be truly clear is to add "re-run this every
> > time you configure" to that notice.
> Jason: didn't we(you) do something like this earlier? I know we
> encountered
> this problem with another user....

This is the message printed each time configure is run:

# For AmberTools 1.5 + Amber 11, print a message about running
if [ -d ../../src/sander ]; then
   echo ""
   echo " NOTE: after installing AmberTools, if you want to compile"
   echo " Amber11 using AmberTools 1.5, you must run the "
   echo " script first, e.g.:"
   echo " cd $AMBERHOME; ./; make $installtype"
   echo " (See the Amber11 Users' Manual for full instructions,"
   echo " and be sure to have a backup, since the"
   echo " script will modify your Amber11 files.)"

This should be displayed at the very end of your configure stage, so
hopefully it would be hard to miss. If anyone has automated builds that
automatically configure and make without any user input, it'll be very easy
to miss this...

All the best,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Thu Jun 09 2011 - 07:30:02 PDT
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