On Thu, 2015-05-07 at 06:32 +0000, Ramin Ekhteiari wrote:
> Hi
>
> Below is the contents of AMBERHOME/bin
> acdoctor cpptraj.log make_crd_hg MMPBSA.py.MPI OptC4.py resp sviol2addles cpptraj.MPI makeDIP_RST.cyana mmpbsa_py_nabnmode paramfit respgen teLeap
> add_pdb database makeDIST_RST mm_pbsa_statistics.pl parmcal rism1d test.py
> AddToBox elsize matextract molsurf parmchk rism3d.snglpnt tinker_to_amber
> am1bcc espgen matgen mpinab parmchk2 sander tleap
> amber.csh exceptions.py matmerge mpinab2c parmed.py sander.LES transform
> amber.sh exceptions.pyc matmul MTKppConstants pbsa sander.LES.MPI translate
> ambmask fantasian MCPB nab pdb4amber sander.MPI tss_init
> ambpdb FEW.pl MCPB.py nab2c pdbSearcher saxs tss_main
> antechamber ffgbsa mdgx nc-config PdbSearcher.py saxs_md tss_next
> ante-MMPBSA.py fftw-wisdom mdgx.MPI nccopy prep2xml senergy ucpp
> atomtype fftw-wisdom-to-conf mdnab ncdump prepgen sequenceAligner UnitCell
> bondtype fix_new_inpcrd_vel mdout2pymbar.pl ncgen process_mdout.perl sgldinfo.sh xaLeap
> capActiveSite frcmod2xml mdout_analyzer.py ncgen3 process_minout.perl sgldwt.sh xleap
> charmmgen func minab nef_to_RST PropPDB softcore_setup.py xparmed.py
> charmmlipid2amber.py gbnsr6 mmE new2oldparm protonator sqm yacc
> ChBox hcp_getpdb mm_pbsa_nabnmode new_crd_to_dyn pymdpbsa stats
> cphstats hybrid mm_pbsa.pl new_to_old_crd pytleap stdLib2Sdf
> cpinutil.py makeANG_RST MMPBSA.py nf-config reduce superimposer
> cpptraj makeCHIR_RST mmpbsa_py_energy nmode residuegen sviol
>
> ls $AMBERHOME/lib/python*/site-packages/
> argparse.py chemistry compat24.pyc fortranformat mcpb MMPBSA_mods ParmedTools pymsmtexp.pyc pymsmtmol sanderles
> argparse.pyc compat24.py cpinutils interface mdoutanalyzer mpi4py pymsmtexp.py pymsmtlib sander
>
> Version of Python
> Python 2.4.3
OK, it seems that a change in ParmEd broke Python 2.4 compatibility.
I'll work on a fix.
Thanks for the report,
Jason
P.S. In the meantime, however, might I suggest installing a newer
version of Python on your system. Python 2.4 is, at this point, 11
years old and hasn't been supported since 2008 in any capacity. I plan
on dropping support for Python 2.4 in my codes moving forward, as Python
2.4 is becoming unusable for scientific applications.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu May 07 2015 - 06:00:03 PDT
