Hi Bill,
Bugfix 9 for AMBER 11 is pretty complex and probably too complex for patch
to be able to work out on its own. I would seriously suggest just starting
from an new untar of the original distributed tar files and apply the
bugfix.all using the application script. So essentially you would do, into a
brand new directory:
tar xvjf AmberTools-1.4.tar.bz2
tar xvjf Amber11.tar.bz2
export AMBERHOME=/path_to_/amber11
cd $AMBERHOME
wget
http://ambermd.org/bugfixes/AmberTools/1.4/bugfix.all
patch -p0 <bugfix.all
rm -f bugfix.all
wget
http://ambermd.org/bugfixes/11.0/bugfix.all
wget
http://ambermd.org/bugfixes/11.0/apply_bugfix.x
chmod 700 apply_bugfix.x
./apply_bugfix.x bugfix.all
Then just build things again from scratch.
Hope this helps.
All the best
Ross
> -----Original Message-----
> From: Bill Snapko [mailto:bill.snapko.qlogic.com]
> Sent: Thursday, January 06, 2011 1:12 PM
> To: amber.ambermd.org
> Subject: [AMBER] Amber 11 - Bugfix 9
>
> Hello,
>
> I am new to using Amber 11 and would like some help please applying bugfix
> #9 to Amber 11. I think I have successfully applied the AmberTools v1.4
bug
> fixes to the installation. No problems or reject files were created. I
have also
> applied bugfix 1 - 8 to the Amber 11 installation without reject files.
>
> The command used for applying the patches is generally
> patch -p0 -N < /path/to/amber/bugfix.Number
>
> The command is issued in the $AMBERHOME directory.
>
> My issue is that bugfix 9 does not apply without failures. Is this normal
to
> expect bugfix 9 to create hunk failures? I have counted 23 failures
reported
> from the patch command. I have attempted to search through the mail
> archives and did not turn up much information on bugfix 9 problems.
>
> This is an excerpt of the output from the patch command with bugfix 9
> patching file src/pmemd/src/cuda/kCPNE.h
> Hunk #2 FAILED at 57.
> Hunk #3 FAILED at 242.
> Hunk #4 FAILED at 368.
> Hunk #5 FAILED at 433.
> 4 out of 5 hunks FAILED -- saving rejects to file
> src/pmemd/src/cuda/kCPNE.h.rej
>
> Please let me know if additional information is required.
>
> Thank you for your help.
> Bill
>
>
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Received on Thu Jan 06 2011 - 13:30:04 PST
