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dimchris / mdanalysis

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does not load psf generated from VMD (possibly related to issue 107) #121

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
### What steps will reproduce the problem? ###

Issue with PSF from VMD
------------------------------------------------------------------------------
Read files from *.ncdf and *.prmtop                        (works)
Stripped unnecessary atoms and wrote dcd                   (works)
Did not know how to generate PSF using MDAnalysis
Generated PSF using VMD
DCD and PSF load fine in VMD
DCD and PSF do not read into Universe( )                   (does not work)
------------------------------------------------------------------------------
Main problem:
------------------------------------------------------------------------------
>>> test_u=Universe(psf_test, dcd_test)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/avanwart/python-environments/epd/lib/python2.7/site-packages/MDAnalysis-0.7.6-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py", line 1910, in __init__
    self._build_segments()
  File "/home/avanwart/python-environments/epd/lib/python2.7/site-packages/MDAnalysis-0.7.6-py2.7-linux-x86_64.egg/MDAnalysis/core/AtomGroup.py", line 1969, in _build_segments
    if seg[0].isdigit():
IndexError: string index out of range
------------------------------------------------------------------------------

The following files are attached for use (they work in VMD- 10 frames).  I have 
looked for fixes on this board "issue 107" and already verified changes 
"package/MDAnalysis/__init__.py" and "package/MDAnalysis/core/PSFParser.py".

dcd_test='dcd_test.dcd'
psf_test='psf_test.psf'

### What is the expected output? What do you see instead? ###

DCD and PSF do not read into Universe( )                   (does not work)

### What version of the product are you using? On what operating system? ###

Linux x86_64

### Please provide any additional information below. ###

It would be nice to either have a fix for this or to be provided with a link on 
how to generate a standard psf format from the *.ncdf and *prmtop files using 
MDAnalysis.

Original issue reported on code.google.com by atvanw...@gmail.com on 13 Dec 2012 at 12:41

Attachments:

GoogleCodeExporter commented 9 years ago 
This issue was closed by revision 1c85077ff7cf.

Original comment by orbeckst on 13 Dec 2012 at 2:16