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
$AMBERHOME/dat/leap/cmd/leaprc.ff99SB" but that is not a valid directory. I
did some searching around in the files and teh correct command is
"$AMBERHOME/AmberTools/src/leap/xleap -s -f
$AMBERHOME/dat/leap/cmd/leaprc.ff99SB"
Thanks
On Sun, Jan 27, 2013 at 12:42 AM, Jonathan Saboury <jsabou1.gmail.com>wrote:
> Hello, all I want to do is use this .pdb:
> http://pastebin.com/iquutx4h
>
> to make a ".prmtop" and ".inpcrd" file so I can input it into OpenMM.
>
> I am an Intermediate C++ programmer but only know hwo to use windows. I am
> using
> the cygwin installation guide "http://ambermd.org/mswindows.html"
>
> Here is the error I am getting.
> http://pastebin.com/9XBk1BDD
>
> Any idea what went wrong? I didn't update bc when I do I get this:
> http://pastebin.com/z75UuTKE
>
> Thanks!
>
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Received on Sun Jan 27 2013 - 12:00:02 PST
