Hi,
http://ambermd.org/tutorials/
Particularly tutorial B1 should help you get started.
On Sun, Oct 30, 2011 at 3:45 AM, James Starlight <jmsstarlight.gmail.com> wrote:
> Also It's not quite understand for me how properly run different amber
> tools programs.
>
> E..g from subdirectory /own/Documents/amber11/AmberTools/bin
> I can run all programs but from another directory that programs are not
> aviable ( I've add the Bin to the path but it didnt work )
For AmberTools to work properly you need to both set the environment
variable AMBERHOME and add $AMBERHOME/bin to your path. For bash this
is:
export AMBERHOME=/own/Documents/amber11
export PATH=$AMBERHOME/bin:$PATH
For tcsh/csh this is:
setenv AMBERHOME /own/Documents/amber11
setenv PATH $AMBERHOME/bin:$PATH
> Finally as I understood LEAP have GUI. How I can run this one ?
Use xleap. To view the molecule once you've created/loaded it, use the
'edit' command, e.g.:
source leaprc.ff10
m = loadpdb mypdb.pdb
edit m
See the AmberTools manual for more details. One note: due to a small
bug in xleap make sure NUMLOCK is off in order to properly access the
menus. Good luck!
-Dan
--
-------------------------
Daniel R. Roe, PhD
Postdoctoral Associate
BioMaPS Institute, Rutgers University
610 Taylor Road
Piscataway, NJ 08854
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Received on Sun Oct 30 2011 - 07:30:03 PDT
