[phenixbb] Error building Amber interface to phenix

Roger Shek roger.shek at stonybrook.edu
Fri Jul 27 14:03:59 PDT 2018


I am trying to build the amber interface to phenix, but encounter an error.
Running OpenSUSE15. Anyone have any ideas?

phenix.build_amber_interface

 Phenix modules found : /opt/phenix-1.13-2998/modules/phenix

 $AMBERHOME set : /home/roger/bin/Amber/amber18

 Linking AMBERHOME to Phenix modules

 Not linking $AMBERHOME into Phenix modules directory because there is
 already a link and it points to the same directory as $AMBERHOME.
   $AMBERHOME : /home/roger/bin/Amber/amber18
   Phenix link: /opt/phenix-1.13-2998/modules/amber

Building amber_adaptbx

 ~> libtbx.configure amber

Python: 2.7.14 "/opt/phenix-1.13-2998/base/bin/python2.7"
Compiler: default
Build mode: release
Warning level: 0
Precompiled Headers: False
Static libraries: False
Static exe: False
Scan Boost headers: False
Write full flex_fwd.h files: False
Build Boost.Python extensions: True
Define BOOST_PYTHON_NO_PY_SIGNATURES: False
Define BOOST_PYTHON_BOOL_INT_STRICT: True
Enable OpenMP if possible: False
Boost threads enabled: False
Enable CUDA: False
Use opt_resources if available: False
Use environment flags: False
Enable C++11: False
Python3 migration warning policy: None
command_version_suffix: 1.13-2998
Relocatable paths anchored at: /opt/phenix-1.13-2998/build
Top-down list of all modules involved:
 prime              "/opt/phenix-1.13-2998/modules/cctbx_project/prime"
 iota               "/opt/phenix-1.13-2998/modules/cctbx_project/iota"
 xia2               "/opt/phenix-1.13-2998/modules/xia2"
 xfel               "/opt/phenix-1.13-2998/modules/cctbx_project/xfel"
 dials              "/opt/phenix-1.13-2998/modules/dials"
 simtbx             "/opt/phenix-1.13-2998/modules/cctbx_project/simtbx"
 cma_es             "/opt/phenix-1.13-2998/modules/cctbx_project/cma_es"
 labelit            "/opt/phenix-1.13-2998/modules/labelit"
 rstbx              "/opt/phenix-1.13-2998/modules/cctbx_project/rstbx"
 spotfinder
        "/opt/phenix-1.13-2998/modules/cctbx_project/spotfinder"
 annlib+adaptbx     "/opt/phenix-1.13-2998/modules/annlib"
                    "/opt/phenix-1.13-2998/modules/annlib_adaptbx"
 phenix             "/opt/phenix-1.13-2998/modules/phenix"
 reel               "/opt/phenix-1.13-2998/modules/reel"
 wxtbx              "/opt/phenix-1.13-2998/modules/cctbx_project/wxtbx"
 phaser_regression  "/opt/phenix-1.13-2998/modules/phaser_regression"
 phaser             "/opt/phenix-1.13-2998/modules/phaser"
 tntbx              "/opt/phenix-1.13-2998/modules/tntbx"
 solve_resolve      "/opt/phenix-1.13-2998/modules/solve_resolve"
 muscle             "/opt/phenix-1.13-2998/modules/muscle"
 ksdssp             "/opt/phenix-1.13-2998/modules/ksdssp"
 pulchra            "/opt/phenix-1.13-2998/modules/pulchra"
 phenix_html        "/opt/phenix-1.13-2998/modules/phenix_html"
 phenix_regression  "/opt/phenix-1.13-2998/modules/phenix_regression"
 elbow              "/opt/phenix-1.13-2998/modules/elbow"
 Plex               "/opt/phenix-1.13-2998/modules/Plex"
 PyQuante           "/opt/phenix-1.13-2998/modules/PyQuante"
 crys3d             "/opt/phenix-1.13-2998/modules/cctbx_project/crys3d"
 gltbx              "/opt/phenix-1.13-2998/modules/cctbx_project/gltbx"
 amber+adaptbx      "/opt/phenix-1.13-2998/modules/amber"
                    "/opt/phenix-1.13-2998/modules/amber_adaptbx"
 mmtbx              "/opt/phenix-1.13-2998/modules/cctbx_project/mmtbx"
 suitename          "/opt/phenix-1.13-2998/modules/suitename"
 king               "/opt/phenix-1.13-2998/modules/king"
 probe              "/opt/phenix-1.13-2998/modules/probe"
 reduce             "/opt/phenix-1.13-2998/modules/reduce"
 iotbx              "/opt/phenix-1.13-2998/modules/cctbx_project/iotbx"
 ccp4io+adaptbx     "/opt/phenix-1.13-2998/modules/ccp4io"
                    "/opt/phenix-1.13-2998/modules/ccp4io_adaptbx"
 dxtbx              "/opt/phenix-1.13-2998/modules/cctbx_project/dxtbx"
 cbflib+adaptbx     "/opt/phenix-1.13-2998/modules/cbflib"

"/opt/phenix-1.13-2998/modules/cctbx_project/cbflib_adaptbx"

 smtbx              "/opt/phenix-1.13-2998/modules/cctbx_project/smtbx"
 ucif               "/opt/phenix-1.13-2998/modules/cctbx_project/ucif"
 cctbx              "/opt/phenix-1.13-2998/modules/cctbx_project/cctbx"
 scitbx             "/opt/phenix-1.13-2998/modules/cctbx_project/scitbx"
 fable              "/opt/phenix-1.13-2998/modules/cctbx_project/fable"
 omptbx             "/opt/phenix-1.13-2998/modules/cctbx_project/omptbx"
 boost+adaptbx      "/opt/phenix-1.13-2998/modules/boost"
                    "/opt/phenix-1.13-2998/modules/cctbx_project/boost_adaptbx"

 tbxx               "/opt/phenix-1.13-2998/modules/cctbx_project/tbxx"
 chiltbx            "/opt/phenix-1.13-2998/modules/cctbx_project/chiltbx"
 libtbx             "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx"
Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_amber.sh"
Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_phenix.sh"
Creating files in build directory: "/opt/phenix-1.13-2998/build"
   dispatcher_include_template.sh
   dispatcher_head.sh
Traceback (most recent call last):
 File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
line 2462, in <module>
   warm_start(sys.argv)
 File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
line 2456, in warm_start
   env.refresh()
 File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
line 1615, in refresh
   self.write_lib_dispatcher_head()
 File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
line 1248, in write_lib_disp
atcher_head
   target_file=self.under_build(target_file, return_relocatable_path=True))
 File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py",
line 1146, in write_bin_sh_d
ispatcher
   target_file.chmod(0755)
 File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/path.py", line
279, in chmod
   return os.chmod(abs(self), *args, **kwds)
OSError: [Errno 1] Operation not permitted:
'/opt/phenix-1.13-2998/build/dispatcher_head.sh'



-- 
Roger Shek

Stony Brook University
Graduate Student in Biochemistry and Structural Biology (PhD)
Stony Brook Integrative Structural Biology Organization
<http://sbinststrbio.com/>
Cell: (808) 386-3879
Website: https://www.rogershek.com
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