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
Received on Fri Dec 28 2012 - 09:00:03 PST
