Hi there,
I use the wrefine.py script provided in xplor-NIH tutorial and set
keepwaters = true. The script looks like this:
......
from simulationTools import StructureLoop
def calcOneStructure( structData ):
from waterRefineTools import refine
protocol.initCoords(inputStructures[structData.structNum])
refine(outFilename=structData.filename(),
potList=potList,
coolingParams=rampedParams,
keepWaters=True,
waterResname=waterResname)
pass
StructureLoop(numStructures=len(inputStructures),
pdbTemplate="SCRIPT_STRUCTURE.sa",
structLoopAction=calcOneStructure,
genViolationStats=True,
averagePotList=potList,
averageContext=FinalParams(rampedParams),
averageFitSel="(resid 601:640 or resid 653:752) and (name CA or name C
or name N)",
averageCompSel="(resid 601:640 or resid 653:752) and (not
resname ANI and not name H*)"
).run()
During calculation, I found water was really kept in structures. However,
when calculation was done, water was removed from all structures. How can I
stop this?
--
Qinhong Yu
Ames' Lab
Department of Chemistry
UC Davis
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