-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Oops- I forgot the attachment.
xplor.parseArguments() # check for typos on the command-line
seq = """
LYS ASN TYR LEU ARG VAL VAL GLY ASN MET GLU ALA ARG PHE ALA VAL ALA
THR PRO GLU GLU LEU ALA VAL ASN ASN ASP ASP CYS ALA ILE CYS TRP ASP
SER MET GLN ALA ALA ARG LYS LEU PRO CYS GLY HIS LEU PHE HIS ASN SER
CYS LEU ARG SER TRP LEU GLU GLN ASP THR SER CYS PRO THR CYS ARG MET
SER LEU ASN ILE ALA ASP ASN ASN ARG VAL ARG GLU GLU
"""
import psfGen
psfGen.seqToPSF(seq)
import protocol
protocol.initTopology("ion.top")
protocol.initParams("ion.par")
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 ZCH2
delete atom 1hg end
delete atom 2hg end
delete atom 3hg end
delete atom 4he2 end
! add bond 5ZN+2 1sg
! add bond 5ZN+2 2sg
! add bond 5ZN+2 3SG
! add bond 5ZN+2 4ne2
! add angle 1SG 5ZN+2 2SG
! add angle 1SG 5ZN+2 3SG
! add angle 1SG 5ZN+2 4ne2
! add angle 2SG 5ZN+2 3SG
! add angle 2SG 5ZN+2 4ne2
! add angle 3SG 5ZN+2 4ne2
! add angle 1CB 1SG 5ZN+2
! add angle 2CB 2SG 5ZN+2
! add angle 3CB 3SG 5ZN+2
! add angle 4cd2 4ne2 5ZN+2
! add angle 4ce1 4ne2 5ZN+2
end
presidue ZCH3
! new for zinc-2
delete atom 6hg end
delete atom 7hg end
delete atom 8hg end
delete atom 9he2 end
! add bond 5ZN+2 6sg
! add bond 5ZN+2 7sg
! add bond 5ZN+2 8SG
! add bond 5ZN+2 9ne2
! add angle 6SG 5ZN+2 7SG
! add angle 6SG 5ZN+2 8SG
! add angle 6SG 5ZN+2 9ne2
! add angle 7SG 5ZN+2 8SG
! add angle 7SG 5ZN+2 9ne2
! add angle 8SG 5ZN+2 9ne2
! add angle 6CB 6SG 5ZN+2
! add angle 7CB 7SG 5ZN+2
! add angle 8CB 8SG 5ZN+2
! add angle 9cd2 9ne2 5ZN+2
! add angle 9ce1 9ne2 5ZN+2
! end zinc-2
! add improper +HA1 +HA2 -SG +C !stereo CA
end
end
!add the PHO groups
segment
setup=true
number=300
chain
sequence ZN2 ZN2 end
end
end
!param
! bond s zn+2 500.0 2.30
! bond NB zn+2 500.0 2.30 !FIX!
! angle s zn+2 s 500.0 109.0
! angle NB zn+2 NB 500.0 109.0
! angle NB zn+2 S 500.0 109.0
! angle CT S ZN+2 500.0 107.94
! angle CV NB ZN+2 500.0 107.94 ! FIX!
! angle CR NB ZN+2 500.0 107.94 ! FIX!
!end
!do patch
patch ZCH2 reference=1=(resid 29)
reference=2=(resid 32)
reference=3=(resid 52)
reference=4=(resid 49)
reference=5=(resid 300) end
patch ZCH3 reference=6=(resid 44)
reference=7=(resid 63)
reference=8=(resid 66)
reference=9=(resid 46)
reference=5=(resid 301) end
""")
xplor.command("write psf output=z2c3h.psf end")
import protocol
protocol.genExtendedStructure()
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("z2c3h.pdb").write()
--- Begin Message ---
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hello Klara--
> I am looking for parameters for zinc ion coordinated by cysteines and
> histidines. So far I found only zinc coordinated by 4 cysteines in
> toph19.ion. Are there parameters for histidine coordination anywhere
> too? Is there a patch that I could use?
You might have a look at the patch in this file- for Zn bound to 2 His
and 2 Cys. I think you should be able to figure out the other cases from
this one.
best regards--
Charles
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.9 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/>
iEYEARECAAYFAkoR3x4ACgkQPK2zrJwS/lYHSwCeMzzqMYCLSOHuqXGBvNUdXmFE
PawAn1dyOVAyQ6PEnGhSRc/c97J2Xj9/
=z8/Z
-----END PGP SIGNATURE-----
--- End Message ---
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1.4.9 (GNU/Linux)
Comment: Processed by Mailcrypt 3.5.8+ <http://mailcrypt.sourceforge.net/>
iEYEARECAAYFAkoR4KoACgkQPK2zrJwS/layEgCeMeqelSERAAsiOkSWSUZw3fqV
/eIAnjlTZ5GldGiLE4ZMpmGHbWW2Syqt
=pZuh
-----END PGP SIGNATURE-----
_______________________________________________
Xplor-nih mailing list
[email protected]
http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih
