Hello Jakob-- > > I am trying to generate a psf file for a small (13 aa) cyclic peptide > based on the template, "eginput/PSF_generation/genCircPep.py". > However, it seems that it is not working: all HT1/HT2/HT3 and OT1/OT2 > are still present in the generated psf file and from careful reading > of the numbers of the bond definitions in the psf-file it seems that > there is defined a bond between resi 1 C and resi 13 N (it should be > the oposite).
Well, that's embarrassing. Clearly, that script was never tested. Please find attached a working version of the script my apologies-- Charles
-- Charles Schwieters email: [email protected] www: http://schwieters.org/cds phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
#
# 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"
import protocol
protocol.initTopology('protein')
protocol.initParams('protein')
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)
xplor.command("""
!make cyclic peptide link
patch PEPT reference=-=(resid 8) reference=+=(resid 1) 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
protocol.writePDB("circ.pdb")
pgpTVxGA4a3rt.pgp
Description: PGP signature
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