Hello,
I was experimenting with manipulating parameters in prmtop files with parmed, and I came across some bizarre behaviour and issues. I was hoping that someone could shed some light or help me fix it.
The first is the use of setBond to change a bond within a LES region. Even if the command is used to "change" a bond by restating its original terms (for example, setBond .x .y aa.00 bb.00, for a bond that already has aa.00 and bb.00 as parameters), it causes the exclusion list to be completely rewritten inside the LES region, changing it dramatically. I'm not sure exactly what it's doing but it's changing something and the resulting prmtop does not seem to work. If the setBond command is used outside a LES region, then it seems to work fine. My questions are, is it possible to manipulate parameters inside a LES region without mucking about with the exclusion list? What exactly is it doing?
The other issue is that, seemingly, the deleteBond command doesn't work. I don't know if it's because I'm missing some library or I compiled it wrong, but no matter the mask or the system, it crashes out of parmed.py with this error:
Traceback (most recent call last):
File "/usr/local/amber14/bin/parmed.py", line 182, in <module>
parmed_commands.cmdloop()
File "/usr/lib/python2.7/cmd.py", line 142, in cmdloop
stop = self.onecmd(line)
File "/usr/lib/python2.7/cmd.py", line 221, in onecmd
return func(arg)
File "<string>", line 1, in <lambda>
File "/usr/local/amber14/lib/python2.7/site-packages/ParmedTools/parmed_cmd.py", line 149, in _normaldo
self.stdout.write('%s\n' % action)
File "/usr/local/amber14/lib/python2.7/site-packages/ParmedTools/ParmedActions.py", line 3500, in __str__
if not self.del_h_bonds and not self.del_noh_bonds:
AttributeError: 'deleteBond' object has no attribute 'del_h_bonds'
Does anyone else see this? I assume this isn't intended behaviour...
Kind regards
Pietro Aronica
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Received on Sun Sep 04 2016 - 21:30:02 PDT
