Hi Joel,
The way I solved this problem was by generating a linear peptide and
then connecting the ends using a LINK card in the header of the pdb.
Good luck!
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On
Behalf Of Joel Tyndall
Sent: Tuesday, February 07, 2012 10:44 PM
To: [email protected]
Subject: [ccp4bb] Generating parameters/cif files for
macrocyclic ligands
Hi folks,
I have an intriguing problem. I'm trying to generate a cif file
for a macrocyclic peptide (of the likes in pdb1d4k
<http://www.rcsb.org/pdb/explore/explore.do?structureId=1d4k> ). They
are cyclic tripeptides units. I can generate a pdb or mol2 file easily.
I have used PRODRG to generate a .cif file and Coot read thjis in
nicely. However, as it is cyclic one cannot adjust the dihedral angles.
I have previously done this using CNS where you can break the tricyclic
peptide into residues and generate parameters to specify bonds/links
between the residues (which allows this kind of movement). I can't come
up with a way to do this without using CNS. I have looked ta J-ligand
which allows for one link "between" two separate residues which
precludes a macrocycle. I have looked at sketcher within CCP4 which
reads the pdb files but I don't believe this can be done here. Within
Coot I can refine the whole ligand but not certain components.
Any suggestions greatly appreciated . ( I may stick to coot
refinement with fixed atoms at this stage)
Regards
Joel
_________________________________
Joel Tyndall, PhD
Senior Lecturer in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
New Zealand
Skype: jtyndall
http://www.researcherid.com/rid/C-2803-2008
Pukeka Matua
Te Kura Taiwhanga Putaiao
Te Whare Wananga o Otago
Pouaka Poutapeta 56 Otepoti 9054
Aotearoa
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