VMD-L Mailing List

From: Birgitte Maria Elisabeth Brydsoe (bbrydsoe_at_hpc2n.umu.se)
Date: Wed Oct 13 2010 - 08:33:00 CDT

I am trying to get IED 2.02 to run under VMD, but have some problems. I
previously tried the binary version of VMD, but could not get it to work.
I have now built VMD 1.8.7 from source, but I still cannot run IED.

I use:

1) CentOS 5.5, 64 bit
2) Downloaded binary VMD 1.8.7 source
3) Installed with tcl 8.4/tk 8.4, Python 2.4.3, Numpy 1.4.1

VMD starts fine and IED appears to do so as well:

p-bc9904 [/ied-2.02]$ vmd
Info) VMD for LINUXAMD64, version 1.8.7 (October 12, 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, 8 CPUs detected.
Info) Free system memory: 15490MB (96%)
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Mesa GLX Indirect
Info) Features: STENCIL MDE MTX NPOT PP PS
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), Multitexture (8)
vmd > gopython 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 >

However, when I load the example IED files I get a lot of errors:

Info) Using plugin trr for coordinates from file
/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/ied-2.02/eigenvec.trr
Info) Finished with coordinate file
/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/ied-2.02/eigenvec.trr.
Info) Using plugin pdb for structure file
/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/ied-2.02/stopol.pdb
Info) Using plugin pdb for coordinates from file
/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/ied-2.02/stopol.pdb
Info) Determining bond structure from distance search ...
Info) Finished with coordinate file
/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/ied-2.02/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/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 "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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
"/afs/hpc2n.umu.se/lap/vmd/1.8.7/src/vmd/lib/vmd/scripts/python/Tkinter.py",
line 1340, in __call__
     return apply(self.func, args)
   File "VMD", line 302, in __call__
   File "/usr/lib64/python2.4/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'

The problem seems to be that IED wants to use some things in Numeric that
no longer exists in Numpy? However, VMD could not be installed with
Numeric but needed Numpy, so how is this solved? Is there a version of
numpy that IED will run with?

Thank you, Birgitte Brydso