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madscatt / zazmol

Library for defining molecular objects to create simulation and analysis programs To install: python setup.py install dependencies: numpy, mocker
GNU General Public License v3.0
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Bug in CharmmTopology class #32

Closed madscatt closed 7 years ago

madscatt commented 7 years ago

reading hiv1_gag.pdb (min3.pdb) the following incorrect output is displayed.

>>> import sasmol.system as system
>>> molecule = system.Molecule('min3.pdb')
reading filename:  min3.pdb
num_atoms =  6730
>>> found  1  model(s) or frame(s)
finished reading frame =  1
>>> molecule.check_charmm_atomic_order_reorganize()
["For residue: GLY_GLYP\nthe atom names doesn't match those in the charmm topology file!\n['N', 'HT1', 'HT2', 'HT3', 'CA', 'HA1', 'HA2', 'HN', 'C', 'O']\n['N', 'HT1', 'HT2', 'HT3', 'CA', 'HA1', 'HA2', 'C', 'O']"]
>>> molecule patch_charmm_residue_atoms('GLY','GLYP')
madscatt commented 7 years ago

@hailiangzhang ... can you debug this?

madscatt commented 7 years ago

This may be an issue with sasmol (in sassie_1.0) only. The following tar-ball contains a new saspdbrx that should fix this issue in the 1.0 branch. It also includes a new test for the method responsible for the original bug. This needs to be carefully tested.

saspdbrx_and_test.tar.gz

madscatt commented 7 years ago

@hailiangzhang ... please compare your line by line changes to that in zazmol/src/python/charmm_topology.py

This still fails the test with the same error. Track this down please.

hailiangzhang commented 7 years ago

Attached is the modified "charmm_topology.py" to fix bugs reported in this issue. charmm_topology.py.tar.gz

madscatt commented 7 years ago

Seems to clean up the error now. Passes the single test that exists for the charmm_topology module.