Hi Jason,
i done all these procedure only after fresh install
Does patching manually work patch -p0 -N < bugfix.X ??
On Fri, Dec 28, 2012 at 10:21 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Did you try the tip here:
> http://jswails.wikidot.com/installing-amber12-and-ambertools-12#toc6 ?
> You
> can probably get the proxy address from your web browser (or cluster
> documentation).
>
> My suggestion is to wipe out your amber12 directory and start over,
> extracting fresh tarballs. All of the patches should apply cleanly, and
> bugfix.16 appears not to. Unless you modified cpptraj's main.cpp file,
> something weird happened. If you _did_ modify main.cpp, then this failure
> may be expected, and you can probably add the flag "--ignore-fails" when
> you update your tree in order to push past this error message. (The
> main.cpp.rej file will show you the patch hunks that failed to apply, so
> you can see if you need to apply the fix by hand around your changes).
>
> HTH,
> Jason
>
> On Fri, Dec 28, 2012 at 12:26 AM, BERGY <nucleic81.gmail.com> wrote:
>
> > Hi Jason,
> > I was not able to get the proxy right. though my aptitude updates all
> > recognise the proxy well. so i have downloaded my pacthes in to local
> > folder and did the following to check
> > commented the netwrk checking part in the patch_amber.py, the change the
> > folders to
> >
> > patch_locs = ['/opt/soft/amber12/bugfixes/AmberTools12bugfixes/',
> > '/opt/soft/amber12/bugfixes/amber12bugfixes/']
> >
> > # ./patch_amber.py --patch-level # *comment before downloading bugfixes*
> > Warning: Unknown number of bugfix .patches/Amber_Applied_Patches/bugfix
> > (1).1
> > Latest patch applied to AmberTools12: 7
> > Latest patch applied to Amber12: 7
> >
> >
> > looks like there were few patches already in the purchased package. then.
> > I change the script and after that
> > # ./patch_amber.py --update-tree
> > Warning: Unknown number of bugfix .patches/Amber_Applied_Patches/bugfix
> > (1).1
> > Determining patches to download for AmberTools12
> > Downloading bugfix.8
> > Downloading bugfix.9
> > Downloading bugfix.10
> > Downloading bugfix.11
> > Downloading bugfix.12
> > Downloading bugfix.13
> > Downloading bugfix.14
> > Downloading bugfix.15
> > Downloading bugfix.16
> > Downloading bugfix.17
> > Downloading bugfix.18
> > Downloading bugfix.19
> > Downloading bugfix.20
> > Downloading bugfix.21
> > Downloading bugfix.22
> > Downloading bugfix.23
> > Downloading bugfix.24
> > Downloading bugfix.25
> > Downloading bugfix.26
> > Downloading bugfix.27
> > Downloading bugfix.28
> > Downloading bugfix.29
> > Downloading bugfix.30
> >
> > Determining patches to download for Amber12
> > Downloading bugfix.8
> >
> > Applying AmberTools12 patches
> > Moving bugfix.8 to AmberTools_Applied_Patches
> > Creating file
> > /usr/soft/amber12/amber12/AmberTools/test/cpptraj/Test_Charmm/test.ala3
> > Moving bugfix.9 to AmberTools_Applied_Patches
> > Moving bugfix.10 to AmberTools_Applied_Patches
> > Moving bugfix.11 to AmberTools_Applied_Patches
> > Moving bugfix.12 to AmberTools_Applied_Patches
> > Moving bugfix.13 to AmberTools_Applied_Patches
> > Creating file
> >
> /usr/soft/amber12/amber12/AmberTools/test/parmed/normal_prmtop/final.prmtop
> > Creating file
> >
> >
> /usr/soft/amber12/amber12/AmberTools/test/parmed/normal_prmtop/prmtop.add_AtNum
> > Creating file
> >
> >
> /usr/soft/amber12/amber12/AmberTools/test/parmed/normal_prmtop/prmtop.new_lj
> > Moving bugfix.14 to AmberTools_Applied_Patches
> > Moving bugfix.15 to AmberTools_Applied_Patches
> > Creating file
> > /usr/soft/amber12/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.cpp
> > Creating file
> > /usr/soft/amber12/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.h
> > Error or warning during patching process for
> > .patches/AmberTools_Unapplied_Patches/bugfix.16:
> > 1 out of 1 hunk FAILED -- saving rejects to file
> > AmberTools/src/cpptraj/src/main.cpp.rej
> >
> >
> >
> > # ./patch_amber.py --patch-level
> > Warning: Unknown number of bugfix .patches/Amber_Applied_Patches/bugfix
> > (1).1
> > Latest patch applied to AmberTools12: 15
> > Latest patch applied to Amber12: 7
> >
> > # ./patch_amber.py --check-updates
> > Warning: Unknown number of bugfix .patches/Amber_Applied_Patches/bugfix
> > (1).1
> > AmberTools12 has 15 unapplied patches: 16, 17, 18, 19, 20, 21, 22, 23,
> 24,
> > 25, 26, 27, 28, 29, 30
> > Amber12 has 1 unapplied patches: 8
> >
> >
> > Though few updates have been made. not all the updates accomplished. pls
> > help.
> >
> > regards,
> > bergy.
> >
> >
> > On Fri, Dec 28, 2012 at 5:54 AM, Jason Swails <jason.swails.gmail.com
> > >wrote:
> >
> > > This issue should have been fixed several months ago (see bugfix.25 for
> > > AmberTools 12). You can check if this patch has been applied by
> running
> > > the commands:
> > >
> > > cd $AMBERHOME && ./patch_amber.py --patch-level
> > >
> > > This should return something like:
> > >
> > > $ ./patch_amber.py --patch-level
> > > Latest patch applied to AmberTools12: 30
> > > Latest patch applied to Amber12: 13
> > >
> > > You can use the command
> > >
> > > ./patch_amber.py --check-updates
> > >
> > > to look for updates (and
> > >
> > > ./patch_amber.py --update
> > >
> > > to update your tree).
> > >
> > > My suggestion is to re-configure and re-build in serial (the configure
> > step
> > > should automatically update your distribution using patch_amber.py).
> > >
> > > HTH,
> > > Jason
> > >
> > > On Thu, Dec 27, 2012 at 7:12 AM, BERGY <nucleic81.gmail.com> wrote:
> > >
> > > > Hi All,
> > > > I am trying to do alanine scanning.
> > > >
> > > > *%%%%%%%%%input parameters*
> > > > &general
> > > > startframe= 1, endframe=100, interval=1, verbose=1,
> > > > strip_mask=:WAT:Cl-:Na+
> > > > entropy=0,
> > > > /
> > > > &gb
> > > > igb=5, saltcon=0.1,
> > > > /
> > > > #&pb
> > > > # istrng=0.100, exdi=80, indi=1.0,
> > > > # inp=2, cavity_surften=0.0378, cavity_offset=-0.5692,
> > > > # fillratio=4, scale=2.0,
> > > > # linit=1000,
> > > > # prbrad=1.4,
> > > > # radiopt=1,
> > > > #/
> > > > &alanine_scanning
> > > > mutant_only=1,
> > > > /
> > > >
> > > > *%%%%%%%%input_script*
> > > > MMPBSA.py -O -i test_alascan.in -o test_alascan.out -sp
> > > complex-wat.top
> > > > -cp complex.top -rp receptor.top -lp ligand.top -y
> > last100snapshots.mdcrd
> > > > -mc complex_mutantD.top -ml ligand_mutantD.top
> > > >
> > > > *%%%%%%%%%%The error message*
> > > > Reading command-line arguments and input files...
> > > > Loading and checking parameter files for compatibility...
> > > > mmpbsa_py_energy found! Using
> > /usr/soft/temp/amber12/bin/mmpbsa_py_energy
> > > > cpptraj found! Using /usr/soft/temp/amber12/bin/cpptraj
> > > > Preparing trajectories for simulation...
> > > > Mutating trajectories...
> > > > AttributeError: 'amberParm' object has no attribute 'name'
> > > > Exiting. All files have been retained.
> > > >
> > > > Please help me out.
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > Jason M. Swails
> > > Quantum Theory Project,
> > > University of Florida
> > > Ph.D. Candidate
> > > 352-392-4032
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Sat Dec 29 2012 - 00:30:02 PST
