To add a Ca2+ ion to my structure, I downloaded the .top and .par
files from HIC-Up, and generated a PSF. Then I patched it into the
calculation with:
xplor.command("parameter @calcium.par end")
xplor.command("structure @calcium.psf end")
xplor.command("coordinates @calcium.pdb end")
My first question is: shouldn't there be files akin to the ion.param
and ion.top files for CNS? I couldn't find something analogous in the
toppar directory. My solution seemed clumsy.
The ion was incorporated into the calculation alright, but the
program crashed at the last line of the calcOneStructure routine:
loopInfo.writeStructure(potList)
My second question is: why did it crash? The program writes a
filename_0.pdb.viols file, but it's empty.
The program writes two tracebacks to standard error. One of them ends
with:
lookupVector[i] = chemTypeLookup[ sim.atomByID(i).chemType() ]
KeyError: 'CA_1'
Which seems potentially intelligible (but still beyond me -- all i
know is that the .psf and .par files have atom, residue, and chain
names that seem to be harmonious with each other).
The second traceback ends with:
File "/usr/local/packages/xplor-nih-2.16.4/python/wrappers/
xplorPot.py", line 119, in rms
def rms(*args): return _xplorPot.XplorPot_rms(*args)
TypeError: PyConvert error: PyXplorPot_Delegate: calcPotData: python
exception
PyInterp::command: error executing: >execfile('gb1-anneal-clean.py')<
I thought the tracebacks implied that the error had to do with the
analysis of the output or something high-level -- the writeStructure
function does act on potList. So I tried to write a crude PDB by
replacing the loopInfo.writeStructure(potList) with xplor.command
(write coordinates output=test.pdb end) and this worked, but now my
file names are not being incremented properly -- how do I pass the
python-level filename to the xplor command?
Thanks,
Ryan
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