From: Ramin Ekhteiari <>
Date: Thu, 7 May 2015 06:32:34 +0000 (UTC)


Below is the contents of AMBERHOME/bin
acdoctor          cpptraj.log       make_crd_hg          resp             sviol2addles              cpptraj.MPI       makeDIP_RST.cyana  mmpbsa_py_nabnmode     paramfit          respgen         teLeap
add_pdb              database           makeDIST_RST  parmcal          rism1d
AddToBox          elsize           matextract          molsurf             parmchk          rism3d.snglpnt     tinker_to_amber
am1bcc              espgen           matgen          mpinab             parmchk2          sander         tleap
amber.csh       matmerge          mpinab2c             sander.LES         transform          exceptions.pyc       matmul          MTKppConstants         pbsa          sander.LES.MPI     translate
ambmask              fantasian           MCPB              nab             pdb4amber          sander.MPI         tss_init
ambpdb               nab2c             pdbSearcher      saxs             tss_main
antechamber          ffgbsa           mdgx              nc-config         saxs_md         tss_next          fftw-wisdom       mdgx.MPI          nccopy             prep2xml          senergy         ucpp
atomtype          fftw-wisdom-to-conf  mdnab          ncdump             prepgen          sequenceAligner    UnitCell
bondtype          fix_new_inpcrd_vel    ncgen             process_mdout.perl         xaLeap
capActiveSite          frcmod2xml  ncgen3             process_minout.perl         xleap
charmmgen          func           minab          nef_to_RST         PropPDB  gbnsr6           mmE              new2oldparm         protonator          sqm             yacc
ChBox              hcp_getpdb       mm_pbsa_nabnmode   new_crd_to_dyn         pymdpbsa          stats
cphstats          hybrid           new_to_old_crd         pytleap          stdLib2Sdf          makeANG_RST          nf-config             reduce          superimposer
cpptraj              makeCHIR_RST       mmpbsa_py_energy   nmode             residuegen          sviol

ls $AMBERHOME/lib/python*/site-packages/   chemistry    compat24.pyc  fortranformat    mcpb           MMPBSA_mods  ParmedTools   pymsmtexp.pyc  pymsmtmol  sanderles
argparse.pyc  cpinutils     interface    mdoutanalyzer  mpi4py  pymsmtlib     sander

Version of Python
Python 2.4.3


     On Thursday, May 7, 2015 4:47 AM, Jason Swails <> wrote:

 On Wed, May 6, 2015 at 5:06 PM, Ramin Ekhteiari <> wrote:

> I have addressed "the path of AMBERHOME" by export
> AMBERHOME=/RS/users/myurtsever/stbknm/amber12/amber15tools/amber14
> and have sourced the (source
> /RS/users/myurtsever/stbknm/amber12/amber15tools/amber14/
> But the same problem has been appeared.

What are the contents of $AMBERHOME/bin?  (Type "ls $AMBERHOME/bin" and
print the contents here).

Also, what are the results of the following commands:

python --version
ls $AMBERHOME/lib/python*/site-packages/
python -m MMPBSA_mods

> ​​
> Interestingly on this system I use ambertools 13 and it works well, but I
> do not know why the new version (15) does not.

​The location where Python modules are stored was changed from
$AMBERHOME/bin to $AMBERHOME/lib/pythonX.X/site-packages, and the
file appropriately updates your environment for this change.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu May 07 2015 - 00:00:03 PDT
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