Re: [phenixbb] Error building Amber interface to phenix

Roger The script is trying to change the mode of a file in /opt/phenix-1.13-2998/build but you don't have that access. Can you get access or get your sys admin to run the script? Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Fri, Jul 27, 2018 at 2:07 PM Roger Shek wrote:

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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]