Re: [AMBER] regarding ambertools

From: Jason Swails <>
Date: Sat, 20 Mar 2010 10:51:54 -0400

Hello Asfa,

Set AMBERHOME to /root/amber11 . No amber programs actually use
$AMBERHOME after the compilation process. The only thing that you'll
want to make sure about is that /root/amber9/exe is in your PATH so
that you can find the executables (sander, pmemd, etc.). However,
make sure that $AMBERHOME/bin (which points to amber11) is in your
PATH before /root/amber9 so that the ambertools 1.3 executables are
found first. e.g.

export AMBERHOME=/root/amber11
export PATH=$AMBERHOME/bin\:/root/amber9/exe\:$PATH

This will make sure that when you type "ptraj", you are getting
/root/amber11/bin/ptraj, and when you type "sander" you are getting
/root/amber9/exe/sander. You can verify this with the "which"

I hope this helps,

On Fri, Mar 19, 2010 at 1:52 PM, Asfa Ali <> wrote:
> Hi,
> I have Amber9 installed in my system. In order to run simulations on pdb
> structures (version 3), I have installed the recent AmberTools 1.3, as
> advised by the ambergroup. In my .bashrc file, I had already set the
> environment for amber9 by:
>              export AMBERHOME=/root/amber9
>              export PATH=/root/amber9/exe:$PATH
> Now in order to work with Ambertools1.3, would I need to again set the
> environment by :
>              export AMBERHOME=/root/amber11
> What else should i write in the bashrc file? Will this ambertools1.3 (which
> is downloaded as amber11) interfere with the running of amber9? Actually I
> need to use leaprc.ff99bsc0 as the force field which is present in
> ambertools1.3 but not in amber9.
> Plz help.
> Thanks,
> Asfa.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sat Mar 20 2010 - 08:00:03 PDT
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