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
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Received on Thu Dec 27 2012 - 16:30:03 PST
