Guillermo,
Thanks you. Your comments were very helpful.
Rather than use the genExtendedStructure() method, I have tried to recreate
the minimization procedure from the old-school script. To my eyes, the
resulting PDB looks reasonable.
(As you are well aware) I don't really know what I'm doing with the python
interface, but they say 1000 monkeys at 1000 typewriters can produce
Hamlet, so chipped away at it using the contents of eginput as templates.
My script is below for anyone in the future facing the same problem.
Thanks again,
Justin
****
xplor.parseArguments()
# Filename for output structures. This string must contain the STRUCTURE
# literal so that each calculated structure has a unique name. The SCRIPT
# literal is replaced by this filename (or stdin if redirected using <),
# but it is optional.
#
outFilename = "extended.pdb"
# The protocol module has many high-level helper functions.
import protocol
protocol.initRandomSeed(331) # set random seed
# Generate PSF from sequence (initialize the correct parameters as side
effect!)
seq = "ACE AIB AIB AIB AIB ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA ALA"
import psfGen
psfGen.residueTypes['protein'].append("AIB")
import protocol
protocol.initTopology('protein')
protocol.initParams('protein')
xplor.command("""
topology
residue AIB
group
atom N type=NH1 charge=-0.36 end
atom HN type=H charge= 0.36 end
group
atom CA type=CT charge= 0.00 end
group
atom CB1 type=CT charge=-0.30 end
atom HB11 type=HA charge= 0.10 end
atom HB12 type=HA charge= 0.10 end
atom HB13 type=HA charge= 0.10 end
group
atom CB2 type=CT charge=-0.30 end
atom HB21 type=HA charge= 0.10 end
atom HB22 type=HA charge= 0.10 end
atom HB23 type=HA charge= 0.10 end
group
atom C type=C charge= 0.48 end
atom O type=O charge=-0.48 end
bond N HN
bond N CA
bond CA CB1 bond CB1 HB11 bond CB1 HB12 bond CB1 HB13
bond CA CB2 bond CB2 HB21 bond CB2 HB22 bond CB2 HB23
bond CA C
bond C O
improper HB11 HB12 CA HB13 !stereo CB1
improper HB21 HB22 CA HB23 !stereo CB2
end
end
""")
psfGen.seqToPSF(seq,amidate_cterm=True,startResid=0)
protocol.genExtendedStructure()
from potList import PotList
potList = PotList()
from xplorPot import XplorPot
potList.append( XplorPot('VDW') )
potList.append( XplorPot("BOND") )
potList.append( XplorPot("ANGL") )
potList.append( XplorPot("IMPR") )
potList.append( XplorPot("ELEC") )
protocol.massSetup()
from ivm import IVM
dyn = IVM()
def calcOneStructure(loopInfo):
"""Calculate a single structure."""
protocol.initNBond(cutnb=5.5,
rcon=20.0,
nbxmod=2,
repel=0.9)
potList.removeAll()
potList.append( XplorPot("BOND"))
potList.append( XplorPot("ANGL"))
potList.append( XplorPot("VDW"))
protocol.initMinimize(dyn,
potList,
printInterval=10,
numSteps=50)
dyn.run()
potList.append( XplorPot("IMPR"))
protocol.initMinimize(dyn,
potList,
printInterval=10,
numSteps=50)
dyn.run()
protocol.initDynamics(dyn,
bathTemp = 300.0,
numSteps = 50,
stepsize = 0.001,
potList = potList,
printInterval=50)
dyn.run()
protocol.initNBond(rcon=2.0,
nbxmod=3,
repel=0.75)
dyn.run()
protocol.initMinimize(dyn,
potList,
printInterval=25,
numSteps=100)
dyn.run()
protocol.initDynamics(dyn,
bathTemp = 300.0,
numSteps = 500,
stepsize = 0.005,
potList = potList,
printInterval=100)
dyn.run()
potList.append( XplorPot("ELEC"))
protocol.initMinimize(dyn,
potList,
printInterval=50,
numSteps=200)
dyn.run()
loopInfo.writeStructure(potList)
pass
from simulationTools import StructureLoop
StructureLoop(numStructures=1,
doWriteStructures=True,
pdbTemplate=outFilename,
structLoopAction=calcOneStructure,
).run()
_______________________________________________
Xplor-nih mailing list
[email protected]
https://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
