Hi Its taken me a while to get around to it, but I just ran elbow to create a cif file etc for my inhibitor, but the bond lengths are quite different from what I got from the PRODRUG server, and it seems that the pdb file I got out of elbow has a few problems (COOT doesn't join up the aromatic ring for example because the carbons are now too far away on one part of the ring). I was wondering how the bond lengths are selected? It seems it is giving the aromatic carbons a bond length of 1.5, when my previous file (and phenylalanine for example have 1.3). Also, I still am not 100% sure how to add the CONNECT information to make the ligand able to covalently bind to the protein. Regards Christine
Christine The bond lengths (if you didn't use the --opt option) are taken from quantum chemical calculations to generate a simple force field. One of the problems with the PDB format is the ambiguity of bond orders that can arise. You should run eLBOW and look at the result to check that the bond connections and bond orders are correct. You can then use the --opt option to generate a better geometry for your refinement. Regarding the covalent bonding, you have some options. You can add a CONECT record CONECT *Overview* The CONECT records specify connectivity between atoms for which coordinates are supplied. The connectivity is described using the atom serial number as found in the entry. CONECT records are mandatory for HET groups (excluding water) and for other bonds not specified in the standard residue connectivity table which involve atoms in standard residues. These records are generated by the PDB. *Record Format* COLUMNS DATA TYPE FIELD DEFINITION ------------------------------------------------------- 1 - 6 Record name "CONECT" 7 - 11 Integer serial Atom serial number 12 - 16 Integer serial Serial number of bonded atom 17 - 21 Integer serial Serial number of bonded atom 22 - 26 Integer serial Serial number of bonded atom 27 - 31 Integer serial Serial number of bonded atom You can also use the LINK record but lets try this option first. Nigel -- Nigel W. Moriarty, Ph.D. Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Christine, I would highly recommend using SMILES strings as input in elbow. This eliminates the ambiguities inherent in assigning bond orders using PDB files. Othwerwise you could build the ligand in a molecular modeling package, minimize it using either a force field or quantum mechanics package, leave the hydrogens on so the program can figure out the bond orders if the connect records are absent, and export this as PDB for input into elbow. This approach is a bit redundant, but works too. Cheers, Carsten
-----Original Message----- From: [email protected] [mailto:[email protected]]On Behalf Of Christine Gee Sent: Friday, February 29, 2008 7:28 PM To: [email protected] Subject: [phenixbb] ligand refinement - elbow
Hi Its taken me a while to get around to it, but I just ran elbow to create a cif file etc for my inhibitor, but the bond lengths are quite different from what I got from the PRODRUG server, and it seems that the pdb file I got out of elbow has a few problems (COOT doesn't join up the aromatic ring for example because the carbons are now too far away on one part of the ring). I was wondering how the bond lengths are selected? It seems it is giving the aromatic carbons a bond length of 1.5, when my previous file (and phenylalanine for example have 1.3). Also, I still am not 100% sure how to add the CONNECT information to make the ligand able to covalently bind to the protein. Regards Christine _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (3)
-
Christine Gee -
Nigel W. Moriarty -
Schubert, Carsten [PRDUS]