VMD-L Mailing List

From: J. Rui Rodrigues (joaquim.rodrigues_at_estg.ipleiria.pt)
Date: Wed Apr 07 2010 - 14:01:37 CDT

Dear all,

I am still trying to get IED running in VMD. I have compiled VMD 1.8.7 in linux
(Ubuntu 8.04.4) against standard tcl/tk8.5 libraries using the following options:
LINUX OPENGL FLTK TK LIBTACHYON NETCDF TCL PYTHON PTHREADS NUMPY SILENT
Before that, I compiled Python2.5.5, numpy-1.3.0 and Numeric-24.2.

After doing "gopython ied-2.02/ied.py", the TK window opens correctly, without
any error message. Then I click "Load ED data from files" and choose the sample
data from IED website. Right after loading the trr/pdb files, I get a long list
of errors (see below). What could be the problem?

The documentation for compiling VMD at
http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html states that "VMD has
been tested with Python 2.2 and later, and Numeric 24.2" but says nothing about
numpy, although numpy is necessary to compile VMD with the option NUMPY... which
versions of numpy are known to work with IED?

Thanks for your time,
Rui Rodrigues

--------------------
jrui_at_herbert:~$ vmd
Info) VMD for LINUX, version 1.8.7 (April 6, 2010)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_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, 1 CPU detected.
Info) Free system memory: 326MB (65%)
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: GeForce4 488 Go/AGP/SSE2
Info) Features: STENCIL MDE CVA MTX PP PS GLSL(OV)
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), 3-D (64x64x64), Multitexture (2)
vmd > gopython ied-2.02/ied.py
Info) Starting Python...
Info) Text interpreter now Python

Interactive Essential Dynamics v 2.0 (http://mccammon.ucsd.edu/ied)
Copyright John Mongan <jmongan_at_mccamon.ucsd.edu>, 2003, 2004

Citation: Interactive Essential Dynamics. John Mongan. Journal of
          Computer-Aided Molecular Design. In press.

This library is provided under the LGPL with ABSOLUTELY NO WARRANTY.

Info) Text interpreter now Tcl
vmd >
vmd > Info) Using plugin trr for coordinates from file /home/jrui/eigenvec.trr
Info) Finished with coordinate file /home/jrui/eigenvec.trr.
Info) Using plugin pdb for structure file /home/jrui/stopol.pdb
Info) Using plugin pdb for coordinates from file /home/jrui/stopol.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file /home/jrui/stopol.pdb.
Info) Analyzing structure ...
Info) Atoms: 1001
Info) Bonds: 1066
Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 136
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 8 Protein: 1 Nucleic: 0
VMD:194: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
VMD:201: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 439, in loadFiles
  File "VMD", line 103, in start
  File "VMD", line 201, in doProjections
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
VMD:301: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
VMD:302: DeprecationWarning: PyArray_FromDimsAndDataAndDescr: use PyArray_NewFromDescr.
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode'
Exception in Tkinter callback
Traceback (most recent call last):
  File "/home/jrui/lib/vmd/scripts/python/Tkinter.py", line 1340, in __call__
    return apply(self.func, args)
  File "VMD", line 303, in __call__
  File "/home/jrui/vmd/vmd-1.8.7/lib/python/lib/python2.5/site-packages/Numeric/Numeric.py", line 175, in
put
    multiarray.put (a, ind, array(v, copy=0).astype(a.typecode()))
AttributeError: 'numpy.ndarray' object has no attribute 'typecode' 

--
Webmail ESTG de Leiria (http://webmail.estg.ipleiria.pt)