Hello,
None of the Amber executables (i.e. sander, pmemd, mm_pbsa, etc.)
depend explicitly on AMBERHOME variable being set. Thus, once you're
done installing both (AMBERHOME will have to be set to each directory
for both installations, but configure should? do that for you), you
can have AMBERHOME permanently point to the amber11 directory and just
make sure that your amber10/exe directory is in your path, and you
should be able to use all executables without ever changing any of
your environment variables.
Hope that helps,
Jason
On Sun, Feb 28, 2010 at 3:35 AM, Trevor Gokey <tgokey.sfsu.edu> wrote:
>
> Yes, mixing Ambertools 1.3 with Amber10 won't give you any result s. Since
> Ambertools 1.3 and Amber 10 now have their own separate AMBERHOMEs , here
> is my quick fix to switch to Ambertools 1.3/Amber 10 in a terminal w indow.
>
> In ~/.bashrc (or whatever shell you're usin g), add at the bottom:
>
> alias amt="export AMBERHO ME=/your/path/to/amber11 && source
> $HOME/.bashrc" (again, change for the appropriate shell)
>
> #so as not to be confused with the corporation amd:
>
> alias amm="export AMBERHOME =/your/path/to/amber10 && source
> $HOME/.bashrc" (ditto above)
> So now in a new window, typing amt switches your AMBE RHOME to Ambertools
> 1.3 so you can use the 1.3 version of leap and such and not 1.2. Going back
> to Amber10 just needs a amm to work.
> Note: i f you decided to not open a new window to try it out, type source
> ~/.bashrc in the terminal to reload to make the aliases work.
> Also, you should have:
>
> export PATH="$AMBERHOM E/exe:$PATH"
>
> in there somewhere. This method isn't extremely robust ie you can't run
> anything in Amber 10 while in amt mode, but you can open a new window and
> run amm from there. It works for me so far. Hope it helps!
>
> Trevor
>
> -----<amber-bounces.ambermd.org> wrote: ---- -
>
> To: AMBER Mail ing List <amber.ambermd.org>
> From: Jason Swails <jason.swails.g mail.com>
> Sent by: <amber-bounces.ambermd.org>
> Date: 02/27/2 010 12:46PM
> Subject: Re: [AMBER] Installation error of amber10 after com pile
> Ambertools1.3
> Hello,
> On Sat, Feb 27, 2010 at 3:37 PM, albert albert
> < albertassonke.googlemail.com> wrote:
> > Dear Amber10 users,
> > > I intend to install the new ambertools 1.3, but the installation o f
> amber10
> > fails on ubuntu 9.10. with gfortran....
> It's a lit tle unclear what you're doing here. AmberTools 1.3
> automatically u npacks into an amber11 directory. This should remain
> this way (i.e . do not unpack AmberTools 1.3 into the amber10
> directory). If you have amber10, you must also have AmberTools 1.2
> unpacked in the amber10 directory. AmberTools 1.2 is available for
> download on ambermd.or g.
> If all of that is correct, then make sure you have applied all
> bugfixes, and it may be helpful to look at
> [1]http://ambermd.org/ubuntu.html .
> Good luck!< br>Jason
> --
> ---------------------------------------
> Jason M. Swai ls
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate St udent
> 352-392-4032
> _______________ ________________________5
> F _______
> AMBER mailing list
> AMBER.ambermd.org
> [2]http://lists.ambermd.o rg/mailman/listinfo/amber
>
>
> References
>
> 1. 3D"http://ambermd.or/
> 2. ="http://lists.ambermd.org/mailman/listinfo/amber"
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Feb 28 2010 - 09:30:04 PST
