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MDAnalysis can't handle Amber14 .prmtop files #192

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
What steps will reproduce the problem?
1. Loading of a .prmtop file prepared using Amber14 Tools (tleap, modification 
via parmed.py, etc)

What is the expected output? What do you see instead?
The code should be able to parse the input .prmtop file, but instead it reports 
a FORTRAN error: "ValueError: unrecognized FORTRAN format"

What version of the product are you using? On what operating system?
MDAnalysis0.8.1 on Ubuntu 14.04, as well as CentOS6.3 compute cluster.

Please provide any additional information below.
Amber12 prmtop files are loaded perfectly fine, just the 14 versions give me 
issues.

Original issue reported on code.google.com by sbowe...@hawk.iit.edu on 6 Aug 2014 at 2:06

GoogleCodeExporter commented 9 years ago 
Hi,

could you attach a small sample file that we can use for debugging and testing? 
(Please see ReportingProblems [1] for details on submitting files.)

Do you have any specific insights regarding the changes in the PRMTOP format? I 
found a PDF documenting the PRMTOP format [2] but cannot find a section that 
details changes between format versions.

Cheers,
Oliver

[1] https://code.google.com/p/mdanalysis/wiki/ReportingProblems
[2] http://ambermd.org/prmtop.pdf

Original comment by orbeckst on 31 Aug 2014 at 5:40

GoogleCodeExporter commented 9 years ago

Original comment by orbeckst on 3 Feb 2015 at 11:28

GoogleCodeExporter commented 9 years ago 
I'm happy to have a crack at this if I can get an Amber14 prmtop to try against

Original comment by richardjgowers on 9 Feb 2015 at 8:10

GoogleCodeExporter commented 9 years ago 
Hello everyone,
It appears that I never closed this issue, and I apologize.  It so happens that 
the inability to read the files was unique to the .prmtop I was trying to use 
at the time.  I have been unable to reproduce the error.  Once again, I 
apologize for leaving this issue in limbo.

Original comment by sbowe...@hawk.iit.edu on 10 Feb 2015 at 9:16

GoogleCodeExporter commented 9 years ago 
Closes Issue 192

Thanks for letting us know. 

Oliver

Original comment by orbeckst on 10 Feb 2015 at 10:43

GoogleCodeExporter commented 9 years ago

Original comment by orbeckst on 11 Feb 2015 at 5:12