VMD-L Mailing List

From: Birgitte Maria Elisabeth Brydsoe (bbrydsoe_at_hpc2n.umu.se)
Date: Wed Oct 13 2010 - 09:28:13 CDT

Sorry, I was unclear in my description. The word 'binary' should not be in
item 2). I did compile from source :)

Thanks, Birgitte

On Wed, 13 Oct 2010, Axel Kohlmeyer wrote:

> 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.
>
>