Hi Christina,
Are you certain this copy of amber hasn't been modified in some way?
Here is what I tried on Kraken just now:
1) Copy Amber10.tar.bz2 from website download to home directory
2) tar xvjf Amber10.tar.bz2
3) cd amber10
4) wget
http://ambermd.org/bugfixes/10.0/bugfix.all
5) patch -p0 -N -r patch_rejects <bugfix.all
This works fine and all files get patched.
Then I tried:
1) cd ..
2) rm -rf amber10
3) tar xvjf Amber10.tar.bz2
4) cd amber10
5) wget
http://ambermd.org/bugfixes/10.0/bugfix.all
6) edit bugfix.all and remove bugfixes 11 and 12
7) patch -p0 -N -r patch_rejects <bugfix.all
8) rm -f bugfix.all
9) wget
http://ambermd.org/bugfixes/10.0/bugfix.all
10)patch -p0 -N -r patch_rejects <bugfix.all
The second patching here (which is essentially what you are trying gives the
following output:
patching file src/sander/evb_umb.f
Reversed (or previously applied) patch detected! Skipping patch.
4 out of 4 hunks ignored -- saving rejects to file patch_rejects
patching file src/sander/evb_umb_primitive.f
Reversed (or previously applied) patch detected! Skipping patch.
....
....
Reversed (or previously applied) patch detected! Skipping patch.
1 out of 1 hunk ignored -- saving rejects to file patch_rejects
patching file src/sander/softcore.f
patching file src/sander/depend
patching file src/sander/sander.f
Hunk #2 succeeded at 743 (offset 9 lines).
patching file test/softcore/complex/out.0.save
patching file test/softcore/complex_rst/out.0.save
patching file test/softcore/complex_rst/out.1.save
patching file test/softcore/dynlmb/out.0.save
patching file test/softcore/dynlmb/out.1.save
patching file test/softcore/min/out.0.save
patching file test/softcore/min/out.1.save
patching file test/softcore/short_md/out.0.save
patching file test/softcore/short_md/out.1.save
patching file test/softcore/short_md/out2.0.save
patching file test/softcore/short_md/out2.1.save
patching file test/softcore/complex/out.1.save
patching file src/sander/softcore.f
Which correctly applies the patch so I'm not sure why it doesn't work
properly for you. Can you try again from a vanilla copy of AMBER 10 please.
All the best
Ross
From: Christina Bergonzo [mailto:cbergonzo.gmail.com]
Sent: Monday, December 08, 2008 5:35 AM
To: ross.rosswalker.co.uk
Subject: bugfix 11 & 12
Good morning,
I tried to apply bugfixes 11 and 12 to a version of amber10 on kraken,
I get the same error when i try to apply both patches (the error below is
from bugfix.11):
can't find file to patch at input line 401
Perhaps you used the wrong -p or --strip option?
The text leading up to this was:
|--- test/softcore/complex_rst/out.0.save 2008-11-10
15:37:09.000000000 -0800
|+++ test/softcore/complex_rst/out.0.save 2008-11-10
15:37:21.000000000 -0800
File to patch:
What file do I need to specify here?
This is a version of amber10 that was compiled on kraken with no errors and
with bugfixed 1-10 successfully applied.
Since I saw your name on bugfix.12, I figured you would know what's up.
Thanks for your help,
Christina Bergonzo
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
to majordomo.scripps.edu
Received on Wed Dec 10 2008 - 01:12:33 PST
