<div dir="ltr">I am trying to build the amber interface to phenix, but encounter an error. Running OpenSUSE15. Anyone have any ideas?<div><br></div><div><span style="font-family:monospace"><span style="color:rgb(0,0,0);background-color:rgb(255,255,255)">phenix.build_amber_interface </span><br>
<br> Phenix modules found : /opt/phenix-1.13-2998/modules/phenix
<br>
<br> $AMBERHOME set : /home/roger/bin/Amber/amber18
<br>
<br> Linking AMBERHOME to Phenix modules
<br>
<br> Not linking $AMBERHOME into Phenix modules directory because there is
<br> already a link and it points to the same directory as $AMBERHOME.
<br> $AMBERHOME : /home/roger/bin/Amber/amber18
<br> Phenix link: /opt/phenix-1.13-2998/modules/amber
<br> <br>Building amber_adaptbx
<br>
<br> ~> libtbx.configure amber
<br>
<br>Python: 2.7.14 "/opt/phenix-1.13-2998/base/bin/python2.7"
<br>Compiler: default
<br>Build mode: release
<br>Warning level: 0
<br>Precompiled Headers: False
<br>Static libraries: False
<br>Static exe: False
<br>Scan Boost headers: False
<br>Write full flex_fwd.h files: False
<br>Build Boost.Python extensions: True
<br>Define BOOST_PYTHON_NO_PY_SIGNATURES: False
<br>Define BOOST_PYTHON_BOOL_INT_STRICT: True
<br>Enable OpenMP if possible: False
<br>Boost threads enabled: False
<br>Enable CUDA: False
<br>Use opt_resources if available: False
<br>Use environment flags: False
<br>Enable C++11: False
<br>Python3 migration warning policy: None
<br>command_version_suffix: 1.13-2998
<br>Relocatable paths anchored at: /opt/phenix-1.13-2998/build
<br>Top-down list of all modules involved:
<br> prime "/opt/phenix-1.13-2998/modules/cctbx_project/prime"
<br> iota "/opt/phenix-1.13-2998/modules/cctbx_project/iota"
<br> xia2 "/opt/phenix-1.13-2998/modules/xia2"
<br> xfel "/opt/phenix-1.13-2998/modules/cctbx_project/xfel"
<br> dials "/opt/phenix-1.13-2998/modules/dials"
<br> simtbx "/opt/phenix-1.13-2998/modules/cctbx_project/simtbx"
<br> cma_es "/opt/phenix-1.13-2998/modules/cctbx_project/cma_es"
<br> labelit "/opt/phenix-1.13-2998/modules/labelit"
<br> rstbx "/opt/phenix-1.13-2998/modules/cctbx_project/rstbx"
<br> spotfinder "/opt/phenix-1.13-2998/modules/cctbx_project/spotfinder"
<br> annlib+adaptbx "/opt/phenix-1.13-2998/modules/annlib"
<br> "/opt/phenix-1.13-2998/modules/annlib_adaptbx"
<br> phenix "/opt/phenix-1.13-2998/modules/phenix"
<br> reel "/opt/phenix-1.13-2998/modules/reel"
<br> wxtbx "/opt/phenix-1.13-2998/modules/cctbx_project/wxtbx"
<br> phaser_regression "/opt/phenix-1.13-2998/modules/phaser_regression"
<br> phaser "/opt/phenix-1.13-2998/modules/phaser"
<br> tntbx "/opt/phenix-1.13-2998/modules/tntbx"
<br> solve_resolve "/opt/phenix-1.13-2998/modules/solve_resolve"
<br> muscle "/opt/phenix-1.13-2998/modules/muscle"
<br> ksdssp "/opt/phenix-1.13-2998/modules/ksdssp"
<br> pulchra "/opt/phenix-1.13-2998/modules/pulchra"
<br> phenix_html "/opt/phenix-1.13-2998/modules/phenix_html"
<br> phenix_regression "/opt/phenix-1.13-2998/modules/phenix_regression"
<br> elbow "/opt/phenix-1.13-2998/modules/elbow"
<br> Plex "/opt/phenix-1.13-2998/modules/Plex"
<br> PyQuante "/opt/phenix-1.13-2998/modules/PyQuante"
<br> crys3d "/opt/phenix-1.13-2998/modules/cctbx_project/crys3d"
<br> gltbx "/opt/phenix-1.13-2998/modules/cctbx_project/gltbx"
<br> amber+adaptbx "/opt/phenix-1.13-2998/modules/amber"
<br> "/opt/phenix-1.13-2998/modules/amber_adaptbx"
<br> mmtbx "/opt/phenix-1.13-2998/modules/cctbx_project/mmtbx"
<br> suitename "/opt/phenix-1.13-2998/modules/suitename"
<br> king "/opt/phenix-1.13-2998/modules/king"
<br> probe "/opt/phenix-1.13-2998/modules/probe"
<br> reduce "/opt/phenix-1.13-2998/modules/reduce"
<br> iotbx "/opt/phenix-1.13-2998/modules/cctbx_project/iotbx"
<br> ccp4io+adaptbx "/opt/phenix-1.13-2998/modules/ccp4io"
<br> "/opt/phenix-1.13-2998/modules/ccp4io_adaptbx"
<br> dxtbx "/opt/phenix-1.13-2998/modules/cctbx_project/dxtbx"
<br> cbflib+adaptbx "/opt/phenix-1.13-2998/modules/cbflib"
<br> "/opt/phenix-1.13-2998/modules/cctbx_project/cbflib_adaptbx"
<br> smtbx "/opt/phenix-1.13-2998/modules/cctbx_project/smtbx"
<br> ucif "/opt/phenix-1.13-2998/modules/cctbx_project/ucif"
<br> cctbx "/opt/phenix-1.13-2998/modules/cctbx_project/cctbx"
<br> scitbx "/opt/phenix-1.13-2998/modules/cctbx_project/scitbx"
<br> fable "/opt/phenix-1.13-2998/modules/cctbx_project/fable"
<br> omptbx "/opt/phenix-1.13-2998/modules/cctbx_project/omptbx"
<br> boost+adaptbx "/opt/phenix-1.13-2998/modules/boost"
<br> "/opt/phenix-1.13-2998/modules/cctbx_project/boost_adaptbx"
<br> tbxx "/opt/phenix-1.13-2998/modules/cctbx_project/tbxx"
<br> chiltbx "/opt/phenix-1.13-2998/modules/cctbx_project/chiltbx"
<br> libtbx "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx"
<br>Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_amber.sh"
<br>Processing: "/opt/phenix-1.13-2998/build/dispatcher_include_phenix.sh"
<br>Creating files in build directory: "/opt/phenix-1.13-2998/build"
<br> dispatcher_include_template.sh
<br> dispatcher_head.sh
<br>Traceback (most recent call last):
<br> File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 2462, in <module>
<br> warm_start(sys.argv)
<br> File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 2456, in warm_start
<br> env.refresh()
<br> File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1615, in refresh
<br> self.write_lib_dispatcher_head()
<br> File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1248, in write_lib_disp<br>atcher_head
<br> target_file=self.under_build(target_file, return_relocatable_path=True))
<br> File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/env_config.py", line 1146, in write_bin_sh_d<br>ispatcher
<br> target_file.chmod(0755)
<br> File "/opt/phenix-1.13-2998/modules/cctbx_project/libtbx/path.py", line 279, in chmod
<br> return os.chmod(abs(self), *args, **kwds)
<br>OSError: [Errno 1] Operation not permitted: '/opt/phenix-1.13-2998/build/dispatcher_head.sh'<br>
<br></span><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><span style="font-size:13px">Roger Shek</span><div style="font-size:13px"><br></div><div style="font-size:13px">Stony Brook University</div><div style="font-size:13px">Graduate Student in Biochemistry and Structural Biology (PhD)</div><div style="font-size:13px"><a href="http://sbinststrbio.com/" style="color:rgb(17,85,204);font-size:12.8px" target="_blank">Stony Brook Integrative Structural Biology Organization</a><br></div><div style="font-size:13px">Cell: (808) 386-3879<br></div><div style="font-size:13px">Website: <a href="https://www.rogershek.com" target="_blank">https://www.rogershek.com</a><br></div></div></div></div></div></div></div></div></div></div></div>