VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Oct 13 2010 - 09:23:19 CDT

On Wed, 2010-10-13 at 15:33 +0200, Birgitte Maria Elisabeth Brydsoe

birgitte,

you can only use a "native" python installation
if you compile VMD yourself. otherwise you need
the matching python installation that was used
to compile the VMD package from here:

http://www.ks.uiuc.edu/Research/vmd/plugins/pythonlib/

cheers,
    axel.

wrote:
> 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
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.