On Nov 4, 2012, at 9:37 AM, Fabian Glaser <fglaser.technion.ac.il> wrote:
> Dear all,
>
> I have recently purchased amber, so forgive me if my questions are a little trivial.
>
> I am trying to follow tutorial A8, which starts by uploading tleap program and paths (I am using a mac OSX sytem), the problem is that despite that (I think) I updated correctly the AMBEHOME PATH in my .bash_profile, in which I added the lines:
>
> export AMBERHOME=/Users/fabian/TOOLS/amber/amber12
> export AMBERTOOLS=$AMBERHOME/AmberTools/bin
> export FPOCKET=/Users/fabian/TOOLS/fpocket/fpocket2/bin
>
> PATH=${PATH}:${PDB_TOOLS}:${IUPred_PATH}:${PDB_CENTRALITY}:${AMBERHOME}:${AMBERTOOLS}:${AMBERHOME}/bin
I would only add AMBERHOME/bin to PATH, not AMBERHOME by itself. And none of the AMBERTOOLS variables are necessary (the AmberTools bin directory is just a link to the Amber bin directory).
>
> The tleap program starts with a path problem:
>
> fabian.fabians-imac { ..A8 }-> tleap
> -I: Adding /Users/fabian/TOOLS/amber/amber12/dat/leap/prep to search path.
> -I: Adding /Users/fabian/TOOLS/amber/amber12/dat/leap/lib to search path.
> -I: Adding /Users/fabian/TOOLS/amber/amber12/dat/leap/parm to search path.
> -I: Adding /Users/fabian/TOOLS/amber/amber12/dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
This is normal. If you want to set up a default force field that you ALWAYS want to use, then copy the leaprc for that force field (e.g., leaprc.ff12SB) to the file name leaprc in AMBERHOME/dat/leap/cmd. Or you can copy the leaprc that you want for a specific project in your current working directory.
What I usually do, though, is just write a tleap script in which I source the leaprc I want (leaprc.ff12SB) at the top of the script and load all of the other files I need separately.
Hopefully this will make more sense as you work through the tutorial.
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Nov 04 2012 - 07:30:02 PST
