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
-------------- next part --------------
--
Charles Schwieters email: Charles at Schwieters.org
www: http://schwieters.org/cds
phone: (301) 402-4914 PGP key: http://schwieters.org/cds/pgp.txt
-------------- next part --------------
#
# 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")
-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/pgp-signature
Size: 198 bytes
Desc: not available
Url :
http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20120713/aded5845/attachment.bin
