Hi
folks,
I have an
intriguing problem. I’m trying to generate a cif file for a macrocyclic
peptide (of the likes in pdb1d4k).
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
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