Hi, phenix.elbow might work... from the phenix website: To run eLBOW on a PDB file (containing one molecule)
phenix.elbow input_file.pdb To run eLBOW on a PDB file containing protein and ligands. This will only process the ligands that are unknown to phenix.refine. phenix.elbow input_file.pdb --do-all -Tina On Fri, Jun 10, 2011 at 10:33 AM, pravinkumar jagtap <[email protected]>wrote: > Dear CCP4 users, > I am trying to get library description for a ligand having a > pentacoordinated phosphate in it (for modeling a transition state) but > unable to do so as Sketcher in CCP4 programms fails with an error message of > > > ERROR: nt = 4 for 10 > ERRROR: in subroutine CMP_CRD_M > ERRROR: in subroutine CALC_POLCRD > ERRROR: in subroutine CREATE_BLCRD > > > and the PRODRUG server fails with an error message > > Error in GROMOS atom names/types. > > In Prodrug server, this mainly seems due to the fact that it cant handle > more than 4 connections/atom. I dont know about sketcher. > > Can anybody advice how to do get library for such a ligand? > > Thanks in advance for any suggestion. > > With regards, > Pravin Kumar. > > > >
