Hello,
I am a graduate student of Chinese Academy of Science and I need ambertool
to do some calculation. So I downloaded it from your official websites and
I try to install it in Cygwin for my operating system is Win7 according to
the methods you offered on the websites. But unfortunately I keep meeting a
lot of questions. And now the problem bothering me is that when I typed
$AMBERHOME/patch_amber.py –update-tree, I was told a lot of errors as
follows:
$ $AMBERHOME/patch_amber.py –update-tree
/home/administrator/amber12/patch_amber.py: line 1: #!/usr/bin/env: No
such file or directory
/home/administrator/amber12/patch_amber.py: line 2: $'\r': command not found
/home/administrator/amber12/patch_amber.py: line 26:
This program was written to automatically check for, download, and/or apply
bug
fixes for Amber. There are 4 major modes or functionalities that this script
contains.
--check-updates : checks for updates on the Amber bug fix server
--patch-level : returns which bug fixes have been applied
--download-patches : downloads the patches that have not been applied
--update : downloads the patches that have not been applied and
patch Amber with those patches
This program is initially written with a single, ASCII patch process in
mind,
but is designed to be easily extended to include different bugfix protocols
as
they become necessary (it supports bzip2- and gzip-compressed bug fixes as
well
and will automatically decompress them).
This script was conceptualized and written by Jason Swails from the
research group of Adrian Roitberg, and is released pursuant to the Amber
and/or AmberTools licenses, whichever is applicable (do not remove this
notice).
Acknowledgements/Contributions from others
* Ben Roberts made helpful contributions to the user-interface
* Tyler Luchko made helpful contributions to the user-interface
: No such file or directory
/home/administrator/amber12/patch_amber.py: line 28: from: command not found
/home/administrator/amber12/patch_amber.py: line 29: $'\r': command not
found
/home/administrator/amber12/patch_amber.py: line 61: $'\r': command not
found
/home/administrator/amber12/patch_amber.py: line 62: __version__: command
not found
/home/administrator/amber12/patch_amber.py: line 63: BUGFIX_PREFIX: command
not found
/home/administrator/amber12/patch_amber.py: line 64: patch_locs: command
not found
/home/administrator/amber12/patch_amber.py: line 65:
http://ambermd.org/bugfixes: No such file or directory
/home/administrator/amber12/patch_amber.py: line 66: syntax error near
unexpected token `('
/home/administrator/amber12/patch_amber.py: line 66: `unapplied_patch_loc =
[pat.join('.patches', 'AmberTools_Unapplied_Patches'),
And now I really don't know what can I do, so I hope you can offer me some
help.
Your sincerely
Zhong shun
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jul 14 2012 - 19:30:03 PDT
