Hi Joel Herman is right: If you are refining cyclic peptides then the easiest way is to use link record linking C-terminus with N terminus. the name of the link should be TRANS. Here is an example:
LINK ALA S 21 ASN S 1 TRANS It will force ALA 21 to be linked (with torsion, angles, planes, bonds etc) to ASN 1 of chain S. This way you do not have to create description for large molecule. If you still want to create one molecule and you have mol2 file with coordinates then you can use libcheck to generate full dictionary using following commands libcheck file_mol <mol_file_name> nodist y It should generate fdescription. However I would prefer using link record. this way you keep amino acid names etc intact. If you amino acids are not among existing then you will need to create their description first and declare them peptide. regards Garib On 8 Feb 2012, at 10:33, herman.schreu...@sanofi.com wrote: > 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:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joel > Tyndall > Sent: Tuesday, February 07, 2012 10:44 PM > To: CCP4BB@JISCMAIL.AC.UK > 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). 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 > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
