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Hello Tian--
>
> I tried the example file, it works. But the script is for generation a
> bond between Ca and SG of Cys. Where I can find the file for the
> normal cyclic peptide formation? The topology parameters are
> complicated to me.
>
Hmm. You're right. Attached is a script for your simpler case. Please
let me know how it goes.
Charles
#
# generate PSF and initial pdb w/ correct covalent geometry for
#
# a circular peptide with sequence
# GLY MET SERP ILE TYRP VAL ALA CYS
#
# with a peptide bond linking the N- and C- termini
#
#
xplor.parseArguments() # check for typos on the command-line
seq = " GLY MET SER ILE TYR VAL ALA CYS"
xplor.command("""
segment
SETUP=TRUE
chain
LINK PEPP HEAD - * TAIL + PRO END { LINK to PRO }
LINK PEPT HEAD - * TAIL + * END
sequence %s
end
end
end
""" % seq)
import psfGen
psfGen.seqToPSF(seq)
xplor.command("""
!make cyclic peptide link
patch PEPT reference=-=(resid 1) reference=+=(resid 8) end
""")
import protocol
xplor.command("write psf output=circ.psf end")
import protocol
protocol.initRandomSeed()
protocol.addUnknownAtoms(dyn_stepsize=0.012,dyn_numStepMul=2)
for i in range(4):
try:
protocol.fixupCovalentGeom(useVDW=1,maxIters=400)
break
except Exception, e:
if e.args[0].startswith("Covalent geometry still violated"):
continue
raise
pass
from pdbTool import PDBTool
PDBTool("circ.pdb").write()
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