Dear Amber users,
I’m running into the following error when trying to load a topology file to parmed.py.
Traceback (most recent call last):
File "/usr/local/amber15/bin/parmed.py", line 126, in <module>
amber_prmtop.add_parm(parm)
File "/usr/local/amber15/lib/python2.7/site-packages/ParmedTools/parmlist.py", line 34, in add_parm
parm = load_file(parm)
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/formats/registry.py", line 121, in load_file
return cls.parse(filename, **kws)
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/amber/amberformat.py", line 347, in parse
return LoadParm(filename)
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/amber/readparm.py", line 69, in LoadParm
parm = parm.view(AmberParm)
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/amber/amberformat.py", line 411, in view
return cls.load_from_rawdata(self)
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/amber/_amberparm.py", line 240, in load_from_rawdata
inst.initialize_topology()
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/amber/_amberparm.py", line 196, in initialize_topology
self.load_structure()
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/amber/_amberparm.py", line 384, in load_structure
self._check_section_lengths()
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/amber/_amberparm.py", line 1215, in _check_section_lengths
check_length('ATOMIC_NUMBER', natom, False)
File "/usr/local/amber15/lib/python2.7/site-packages/chemistry/amber/_amberparm.py", line 1204, in check_length
(key, len(self.parm_data[key]), length))
chemistry.exceptions.AmberParmError: FLAG ATOMIC_NUMBER has 303288 elements; expected 7425
I’ve googled the chemistry.exceptions.AmberParmError error message but I haven’t found previous similar issues in the mailing list.
The topology file is the non-hmr version of a trajectory that was done using hmr on a 30Å water box, it contains the protein and counter ions but not water. Now I’m lumping the trajectories together and I’ve also removed the counter ions from them, and that’s why I need to use parmed.py on the topology file to get rid of the Na+ and Cl- atoms as well.
Here’s the topology file if you want to take a look at it:
https://raw.githubusercontent.com/jeiros/Scripts/master/nohmr.prmtop
I’ve also tried to load other topology files I have been using and they give no trouble. So I think something’s wrong with the topology file itself and not parmed.py
Looking forward to your comments,
Juan
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Received on Wed Sep 09 2015 - 11:00:03 PDT
