add Zn2+ atoms to PDB

[Qianwen Li]

Charles,

I'm trying to adding a Zn2C2H2 zinc finger in structure calculation. My first 
step is deleting specific H atoms in CYS and HIS adding Zn2+ to PDB. 
Attachments are the scripts and input and output PDBs.

I want to delete the HD1 in HIS73 and HE2 in HIS75, because ND1 in HIS73 and 
NE2 in HIS75 are coordination atoms.

But the problems is, HE2 of HIS75 still exsts in output PDB and final 
calculations. Please help me check the scripts, if there is problem.

Thanks!

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simWorld.setRandomSeed(5521)

proteinSeq="""
 three character residue name sequence
"""

import psfGen
psfGen.seqToPSF(open('protein.seq').read(),startResid=1)

import protocol
protocol.initTopology('ion')
xplor.command("""

 topology 

 AUTO ANGLe=False DIHEdral=False END 
 
! patch to create Zn (Cys)2 (His)2 
!
! 1 and 2 should be CYS 
!
! 3 and 4 should be HIS 

 presidue ZnC2H2

  delete atom 1hg end 

  delete atom 2hg end 

  delete atom 3hd end 
  
  delete atom 4he end 

  add bond 5ZN+2 1sg 

  add bond 5ZN+2 2sg 

  add bond 5ZN+2 3nd1 

  add bond 5ZN+2 4ne2 

  add angle 1SG  5ZN+2 2SG 

  add angle 1SG  5ZN+2 3nd1 

  add angle 1SG  5ZN+2 4ne2 

  add angle 2SG  5ZN+2 3nd1

  add angle 2SG  5ZN+2 4ne2 
  
  add angle 3nd1 5ZN+2 4ne2  

 end 

end 
 
!add the Zn2 atom
 
segment 

setup=true 

number=401  

chain    

sequence ZN2 end  

end 

end 
!do patch   

patch ZnC2H2  reference=1=(resid 45)              

 reference=2=(resid 50)               

 reference=3=(resid 73)              

 reference=4=(resid 75)              

 reference=5=(resid 401)
end 
 


""")

protocol.initCoords("new_8.pdb")
protocol.initParams("zn-finger_new.par")

protocol.addUnknownAtoms()

# This next line will change the coordinates somewhat, and may not be a
# good idea.
#
protocol.fixupCovalentGeom(maxIters=100,useVDW=1)


xplor.command("write psf output=new.psf end")
protocol.writePDB("new.pdb")

zn-finger_new.par
Description: Binary data

new_8.pdb
Description: application/aportisdoc

new.pdb
Description: application/aportisdoc