I would like to include ensemble files in the water refinement script. I
tried give file names in the script.it doesn't twork.
could you please let me know how to include pdb files in water refinement
script (gb1/rdc/wrefine.py) ?
Thanking you !
xplor.requireVersion("2.26")
inputStructuresGlob="refine_[0-9]*.sa"
# protocol module has many high-level helper functions.
#
import protocol
protocol.initRandomSeed(3421) #explicitly set random seed
import glob
inputStructures=glob.glob(inputStructuresGlob)
#this could also be a list of filenames
"refine_4.pdb,refine_5.pdb,refine_10.pdb,refine_14.pdb,
refine_22.pdb,refine_54.pdb,refine_60.pdb,refine_62.pdb,
refine_72.pdb,refine_27.pdb"
simWorld.setRandomSeed( 785 )
import protocol
backbone="name C or name CA or name N or name O or name HN"
#Nilges topology/parameters
xplor.command('evaluate ($par_nonbonded = "OPLSX")')
protocol.parameters['protein']="waterRef/parallhdg5.3.pro.new"
protocol.parameters['water'] ="waterRef/parallhdg5.3.sol"
protocol.topology['protein'] ="waterRef/topallhdg5.3.pro.new"
protocol.topology['water'] ="waterRef/topallhdg5.3.sol"
waterResname="TIP3"
protocol.initParams(("protein","ion.par"))
#protocol.initStruct("zc2h2_waterref.psf")
protocol.loadPDB(inputStructures[0],deleteUnknownAtoms=True)
from potList import PotList
from simulationTools import MultRamp, StaticRamp, FinalParams
potList = PotList()
rampedParams=[]
--Vas
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