AMBER Archive (2009)

Subject: [AMBER] Re: bugfix 10 failing for ambertools1.2

From: Alan (alanwilter_at_gmail.com)
Date: Mon Jul 20 2009 - 03:25:55 CDT

And bugfix.9 too has problems.

Apparently in both bugfixes the full path the files are not complete:

*** prm.c 2008-04-08 17:10:11.000000000 -0400
--- prm.c 2009-04-23 10:54:51.000000000 -0400

Should be:

*** src/nab/prm.c 2008-04-08 17:10:11.000000000 -0400
--- src/nab/prm.c 2009-04-23 10:54:51.000000000 -0400

But in bugfix.all, bugfix.9 is correct.

I did the right modifications in bugfix.all and it worked for me.

Alan

On Mon, Jul 20, 2009 at 09:14, Alan<alanwilter_at_gmail.com> wrote:
> Hi there,
>
> I am doing this:
>
> tar xvfj AmberTools-1.2.tar.bz2
> cd $AMBERHOME
> wget -c http://ambermd.org/bugfixes/AmberTools/1.2/bugfix.all
> mv -f bugfix.all bugfixAmberTools.all
> patch -p0 -N < bugfixAmberTools.all
>
> patching file test/antechamber/charmm/ala2.prm.save
> patching file src/nab/sff2.c
> patching file src/ptraj/ptraj.c
> patching file src/ptraj/io.c
> patching file src/ptraj/ptraj.c
> patching file src/ptraj/trajectory.h
> patching file src/leap/src/leap/pdb_format.c
> patching file dat/leap/parm/gaff.dat
> patching file src/ptraj/ptraj.c
> patching file src/ptraj/ptraj.c
> Hunk #2 succeeded at 3386 (offset 7 lines).
> Hunk #3 succeeded at 3450 (offset 7 lines).
> Hunk #4 succeeded at 3546 (offset 7 lines).
> Hunk #5 succeeded at 3583 (offset 7 lines).
> Hunk #6 succeeded at 3598 (offset 7 lines).
> Hunk #7 succeeded at 3810 (offset 7 lines).
> Hunk #8 succeeded at 3884 (offset 7 lines).
> Hunk #9 succeeded at 4094 (offset 7 lines).
> Hunk #10 succeeded at 4144 (offset 7 lines).
> Hunk #11 succeeded at 4169 (offset 7 lines).
> Hunk #12 succeeded at 4226 (offset 7 lines).
> Hunk #13 succeeded at 4360 (offset 7 lines).
> Hunk #14 succeeded at 5397 (offset 7 lines).
> Hunk #15 succeeded at 5577 (offset 7 lines).
> Hunk #16 succeeded at 6045 (offset 7 lines).
> patching file src/ptraj/trajectory.h
> patching file src/ptraj/ptraj.c
> patching file src/nab/prm.c
> can't find file to patch at input line 1531
> Perhaps you used the wrong -p or --strip option?
> The text leading up to this was:
> --------------------------
> |
> |********> bugfix.10
> |Author: Dave Case
> |Date: 07/17/2009
> |
> |Programs: tleap
> |
> |Description: fix up the residue numbers in loadMol2 if the input mol2 file
> |             has residue numbers outside the range 1 to number of
> |             substructures
> |             phase angles (as in parmbsc0).  Check for that.  Note that this
> |             effectively undoes bugfix.2
> |
> |Usage: Use this patch to update amber10/src/leap/src/leap/tripos.c
> |
> |------------------------------------------------------------------------------
> |--- tripos.c   15 Apr 2008 23:22:21 -0000      10.0
> |+++ tripos.c   7 Jul 2009 20:04:46 -0000
> --------------------------
> File to patch: ^C
>
> What am I doing wrong?
>
> Many thanks in advance.
>
> Alan
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>>http://www.bio.cam.ac.uk/~awd28<<
> 

-- 
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<

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