Hi Dan,
I'm sorry to get back to you so late. I think this worked; ptraj is telling
me:
PTRAJ: trajin ../production2.traj.gz
Checking coordinates: ../production2.traj.gz
Rank: 0 Atoms: 65467 FrameSize: 1590874 TitleSize: 81 NumBox: 3 Seekable 1
I've never seen the last line before, but I'm assuming it's the new that
AmberTools writes things, right?
I was also wondering why I needed to make sure that I wasn't overwriting the
old copy of AmberTools when I was just going to recompile it anyway. When I
recompiled AmberTools after implementing the bugfix.all patch, I did so in a
different directory from the one where I originally compiled AmberTools. Can
I delete my first version?
Thanks a lot for all your help, Dan. I really appreciate it.
Kamali
On Sun, Feb 6, 2011 at 2:37 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> It seems like the patch is having trouble finding where it is supposed
> to apply itself. This can occur e.g. when patches are applied out of
> order. The patch 'ptraj_2010-07-16-fixFilesize.patch' was an
> unofficial bugfix; I recommend you use the release version of the
> AmberTools 1.4 bugfixes (http://ambermd.org/bugfixesat.html, use
> bugfix.all) as well as a fresh copy of AmberTools 1.4 to ensure the
> patches will be applied successfully. So do something like:
>
> tar -zxf AmberTools.1.4.tgz (make sure you aren't overwriting your old
> version of AmberTools 1.4)
> cd amber11
> patch -p0 -N < bugfix.all (Patching should have no issues at this point)
> cd AmberTools/src
>
> Then configure with whatever options are appropriate for your Mac and
> compile normally. Let me know if you still have issues applying the
> patch or problems with gzipped files after compilation.
>
> -Dan
>
> On Sun, Feb 6, 2011 at 12:51 PM, Kamali Sripathi <ksripath.umich.edu>
> wrote:
> > Hi Dan and fellow AMBER users,
> > I've been having similar problems with ptraj reading in gzipped
> trajectories
> > after installing AmberTools v1.4 on my Mac. I've tried your most recent
> > patch from July 18th, 2010, Dan, but I keep getting this message when I
> type
> > in "patch -p0 -N < ptraj_2010-07-16-fixFilesize.patch":
> > patching file AmberTools/src/ptraj/ptraj.c
> > Hunk #1 FAILED at 2058.
> > Hunk #2 FAILED at 2418.
> > 2 out of 2 hunks FAILED -- saving rejects to file
> > AmberTools/src/ptraj/ptraj.c.rej
> > patching file AmberTools/src/ptraj/io.c
> > Hunk #1 FAILED at 673.
> > Hunk #2 FAILED at 698.
> > Hunk #3 FAILED at 739.
> > Hunk #4 FAILED at 766.
> > Hunk #5 succeeded at 705 (offset -85 lines).
> > Hunk #6 succeeded at 728 (offset -85 lines).
> > 4 out of 6 hunks FAILED -- saving rejects to file
> > AmberTools/src/ptraj/io.c.rej
> > patching file AmberTools/src/ptraj/io.h
> > Hunk #1 FAILED at 76.
> > Hunk #2 FAILED at 97.
> > 2 out of 2 hunks FAILED -- saving rejects to file
> > AmberTools/src/ptraj/io.h.rej
> > I think my problem may be more of a patching problem itself, or also the
> > fact that I might not have compiled AmberTools properly, but I thought
> I'd
> > start ask you, Dan, and Amber Mac users for a start.
> > Thanks a lot, everyone!
> > Kamali
> >
> >
>
>
>
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Received on Fri Feb 11 2011 - 08:00:02 PST
