#
# Number of structures.
#
nstructures = 100 

###EDIT default 100

#
# Read PSF file(s) (or generate from scratch)
#


#
# generate PSF data from sequence and initialize the correct parameters.
#
#from psfGen import seqToPSF
#seqToPSF(open('protG.seq').read())

#
# generate a random extended structure with correct covalent geometry
#
#protocol.genExtendedStructure("gb1_extended_%d.pdb" % seed)

seq = " ACE BIMC ALA ALA CYS"

import protocol
protocol.initTopology(('protein','new.top'))
protocol.initParams(('protein','new.par'))




import psfGen
psfGen.seqToPSF(seq,seqType='prot',startResid=0,amidate_cterm=True)


xplor.command("""
topology
AUTO ANGLe=False DIHEdral=False END

end

!make cyclic link
 patch CBI2 reference=-=(resid 4) reference=+=(resid 1) end
! patch HBI2 reference=-=(resid 6) reference=+=(resid 2) end


""")

import protocol
protocol.genExtendedStructure()
protocol.fixupCovalentGeom(useVDW=1)#,maxIters=1000,angleTol=5,torsionTol=5)

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