On Sun, Jan 27, 2013 at 2:53 PM, Jonathan Saboury <jsabou1.gmail.com> wrote:
> Tried on Ubuntu and was much easier. One edit for this page:
> http://ambermd.org/tutorials/basic/tutorial1/section2.htm on *"2.1.2)
> Loading the structure into Leap*"
> the command stated to put is "$AMBERHOME/exe/xleap -s -f
> $AMBERHOME/dat/leap/cmd/leaprc.ff99SB"
I will fix this. The correct command is $AMBERHOME/bin/xleap -s -f
leaprc.ff99SB. All Amber programs are in $AMBERHOME/bin (which used to be
$AMBERHOME/exe).
Note, we replaced the "exe" directory with the "bin" directory (it's more
Unix-like). Also, the standard leap dat directories are available for
searching by default -- you do not need to specify the path of the leaprcs
unless they are in a different location.
> but that is not a valid directory. I
> did some searching around in the files and teh correct command is
> "$AMBERHOME/AmberTools/src/leap/xleap -s -f
>
This is not the copy of xleap you should use. Use the one in
$AMBERHOME/bin. The copy in the src/ directory should actually not be
executable, IMO (for this reason).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sun Jan 27 2013 - 12:30:03 PST
