Hi Bryon--
>
> 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()
You are omitting important portions of the script: what does
structLoopAction look like?
thanks--
Charles
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