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
>
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Received on Thu Dec 27 2012 - 21:30:02 PST
