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msmbuilder / msmbuilder-legacy

Legacy release of MSMBuilder
http://msmbuilder.org
GNU General Public License v2.0
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SaveStructure.py does not output all 10 structures specified in -k flag, only outputs 1 structure #321

Closed lilipeng closed 10 years ago

lilipeng commented 10 years ago

Error output: File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/mdtraj-0.5.1-py2.7-linux-x86_64.egg/mdtraj/trajectory.py", line 1115, in save_pdb modelIndex=i) File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/mdtraj-0.5.1-py2.7-linux-x86_64.egg/mdtraj/pdb/pdbfile.py", line 259, in write (res.resSeq) % 10000, _format_83(coords[0]), File "/home/lilipeng/epd/epd-7.3-2-rh5-x86_64/lib/python2.7/site-packages/mdtraj-0.5.1-py2.7-linux-x86_64.egg/mdtraj/pdb/pdbfile.py", line 592, in _format_83 'in a width-8 field' % f) ValueError: coordinate "-2.14748e+07" could not be represnted in a width-8 field

Output log:

IS Haque, KA Beauchamp, VS Pande. In preparation. A Fast 3 x N Matrix Multiply Routine for Calculation of Protein RMSD.

{'assignments': 'Assignments.h5', 'conformations_per_state': 1, 'format': 'pdb', 'output_dir': '/home/lilipeng/MSM_kinase/Src/ANS_intermediate/water_traj/RUN0_temp3_protein', 'project': 'ProjectInfo.yaml', 'quiet': False, 'replacement': True, 'states': [-1], 'style': 'sep'} 14:04:52 - Yanking from all 10 states 14:04:55 - Saving file: /home/lilipeng/MSM_kinase/Src/ANS_intermediate/water_traj/RUN0_temp3_protein/State0-0.pdb 14:04:55 - Saving file: /home/lilipeng/MSM_kinase/Src/ANS_intermediate/water_traj/RUN0_temp3_protein/State1-0.pdb

rmcgibbo commented 10 years ago

The position of one of the atoms is at the cartesian coordinate -2.14748e+07, which is too big to represent in a PDB file because of fixed width formatting. Maybe you want to center your coordinates near the origin?

lilipeng commented 10 years ago

Actually I just realized I'd clustered the data using one of the problematic trajectories mentioned in Issue #309. Let me re-cluster the data excluding all problematic trajectories.

On 3 February 2014 14:47, Robert McGibbon notifications@github.com wrote:

The position of one of the atoms is at the cartesian coordinate -2.14748e+07, which is too big to represent in a PDB file because of fixed width formatting. Maybe you want to center your coordinates near the origin?

Reply to this email directly or view it on GitHubhttps://github.com/SimTk/msmbuilder/issues/321#issuecomment-34010177 .

lilipeng commented 10 years ago

Resolved. Issue #321 can now be closed.