VMD-L Mailing List

From: Cun Zhang (apzc2529_at_gmail.com)
Date: Fri Dec 25 2009 - 06:03:46 CST

hi,
I'm trying to use vmd python library in Python. when I run "import VMD" in python,
it returns the following error. Anybody knows what's wrong with it?

Thank you!

Cun Zhang


cunzhang@Debian:~$ ipython
Python 2.5.4 (r254:67916, Nov 19 2009, 22:14:20)
Type "copyright", "credits" or "license" for more information.

IPython 0.10 -- An enhanced Interactive Python.
?         -> Introduction and overview of IPython's features.
%quickref -> Quick reference.
help      -> Python's own help system.
object?   -> Details about 'object'. ?object also works, ?? prints more.

In [1]: import sys

In [2]: sys.path.append("/usr/local/lib/vmd/scripts/python")

In [3]: import VMD
Info) VMD for LINUXAMD64, version 1.8.8a7 (December 25, 2009)
Info) http://www.ks.uiuc.edu/Research/vmd/                        
Info) Email questions and bug reports to vmd@ks.uiuc.edu          
Info) Please include this reference in published work using VMD:  
Info)    Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual  
Info)    Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 4 CPUs detected.
Info) Free system memory: 2444MB (61%)
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pltplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pltplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pltplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pltplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/stlplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/stlplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/stlplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/stlplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gromacsplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gromacsplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gromacsplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gromacsplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/situsplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/situsplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/situsplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/situsplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mapplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mapplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mapplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mapplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/biomoccaplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/biomoccaplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/biomoccaplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/biomoccaplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/fs4plugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/fs4plugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/fs4plugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/fs4plugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pbeqplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pbeqplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pbeqplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/pbeqplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mol2plugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mol2plugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mol2plugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mol2plugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/phiplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/phiplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/phiplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/phiplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dxplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dxplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dxplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dxplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/msmsplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/msmsplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/msmsplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/msmsplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dsn6plugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dsn6plugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dsn6plugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dsn6plugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xsfplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xsfplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xsfplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xsfplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/spiderplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/spiderplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/spiderplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/spiderplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/cubeplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/cubeplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/cubeplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/cubeplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dtrplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dtrplugin.so: undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dtrplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/dtrplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parmplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parmplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parmplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parmplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/maeffplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/maeffplugin.so: undefined symbol: _ZTVN10__cxxabiv120__si_class_type_infoE
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/maeffplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/maeffplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/edmplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/edmplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/edmplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/edmplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/uhbdplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/uhbdplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/uhbdplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/uhbdplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parm7plugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parm7plugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parm7plugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/parm7plugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/ccp4plugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/ccp4plugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/ccp4plugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/ccp4plugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/graspplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/graspplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/graspplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/graspplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/bgfplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/bgfplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/bgfplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/bgfplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mdfplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mdfplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mdfplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/mdfplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/grdplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/grdplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/grdplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/grdplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/brixplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/brixplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/brixplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/brixplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/raster3dplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/raster3dplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/raster3dplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/raster3dplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/avsplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/avsplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/avsplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/avsplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xbgfplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xbgfplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xbgfplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/xbgfplugin.so
ERROR) Unable to open dynamic library '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gridplugin.so'.
ERROR) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gridplugin.so: undefined symbol: __gxx_personality_v0
Unable to dlopen '/usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gridplugin.so':
Unable to dlopen plugin file /usr/local/lib/vmd/plugins/LINUXAMD64/molfile/gridplugin.so

In [4]: