Dear Charles:
I am trying to write a script to add a TEMPO to multiple structures that have
already been docked with another program. My script can modify the first
structure. However, the program ends as it loops back to start on the second
structure. The loop is as follows:
#Dynamics to add TEMPO
def structGen(loopcount):
#Load structure and add TEMPO
protocol.initStruct("./docked.psf")
protocol.initCoords("./water1/docking_%dw.pdb" % (loopcount))
...
xplor.command("write psf output=./mod/tempo%d.psf end" % (loopcount))
outFile = PDBTool("./mod/tempo%d.pdb" % (loopcount))
outFile.write()
return
for i in range(1,101):
structGen(i)
pass
After the XPLOR runs "struct reset end" from protocol.initStruct on the second
loop, the program ends with:
Segmentation fault (core dumped)
If I modify the loop to use StructureLoop from simulationTools, the program
ends after completion of the first structure with the following output:
Traceback (most recent call last):
File "<string>", line 2, in <module>
File "/opt/software/xplor-nih-2.38/python/trace.py", line 180, in run
exec cmd in dict, dict
File "<string>", line 1, in <module>
File "mod.py", line 242, in <module>
StructureLoop(numStructures=2,structLoopAction=structLoopAction).run()
File "/opt/software/xplor-nih-2.38/python/simulationTools.py", line 418, in
run
sim.setAtomPosArr( initCoords )
File "/opt/software/xplor-nih-2.38/python/wrappers/simulation.py", line 98,
in setAtomPosArr
def setAtomPosArr(self, *args, **kwargs): return
_simulation.Simulation_setAtomPosArr(self, *args, **kwargs)
SystemError: xplor-nih error: FIX: setAtomPosArr: array should have size
numAtoms
PyInterp::command: error executing: >execfile('mod.py')<
Any help will be greatly appreciated.
Sincerely,
Bryon
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