AMBER Archive (2008)

Subject: AMBER: RE: bugfix 11 & 12

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Dec 08 2008 - 15:12:42 CST

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_at_gmail.com]
Sent: Monday, December 08, 2008 5:35 AM
To: ross_at_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

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