############################################################################ ## [grade_PDB_ligand] produce grade dictionary for existing PDB ligand ############################################################################ Copyright (C) 2010-2014 by Global Phasing Limited All rights reserved. This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL. Version: 1.2.8 Authors: Smart OS, Womack, TO, Sharff A, Flensburg C, Keller P, Paciorek W, Vonrhein C and Bricogne G To cite: see http://www.globalphasing.com/buster/wiki/index.cgi?GradeCite ------------------------------------------------------------------------------ Acknowledgements: mogul: http://www.ccdc.cam.ac.uk/products/csd_system/mogul/ libcheck: http://www.ccp4.ac.uk/html/libcheck.html QM method uses fdynamo library http://www.pdynamo.org/ to perform calculations using the RM1 method http://www.rm1.sparkle.pro.br/ Setting up external tools needed....(obabel version 2.3.0)..(curl=/usr/bin/curl). Success all external tools are properly setup (for a more thorough check run "grade_PDB_ligand -checkdeps"). Looking for 880 at EBI MSDchem Ligand name: 880 is CYCLOHEXYL-_4-_5-_3,4-DICHLOROPHENYL_-2-PIPERIDIN-4-YL-3-PROPYL-3H-IMIDAZOL-4-YL_-PYRIMIDIN-2-YL_AMINE Converting downloaded ideal pdb to mol2 using obabel version 2.3.0 : 1 molecule converted Now invoking grade to get dictionary: Setting up external tools needed.(test mogul WARNING Test run of mogul has detected that you are using mogul 1.6 (RC5) ....... There is an update available from the CCDC that has significant ....... improvements particularly in computational speed. You are advised ....... to update your CSDS software, for instructions on how to do this ....... please visit: http://www.ccdc.cam.ac.uk/products/csd_system/updates ....... (Note that grade results should be fine until you can upgrade.) ).. Success all external tools are properly setup (for a more thorough check run "grade -checkdeps"). Loading atom-type information from /home/software/GPhL/BUSTER_stable_production_20140512/autoBUSTER/grade-data/sybyl_to_refmac.dat Loading atom-type information from /home/software/GPhL/BUSTER_stable_production_20140512/autoBUSTER/grade-data/sybyl_to_refmac.dat Input is MOL2; assuming that the coordinates in the mol2 are good Run mogul with generalisation_min_relevance=0.9 for bond and angle mogul ran (cpu secs used: 9.9 real, 5.4 user, 2.7 sys) Loaded hybridisations for 55 atom types from /home/software/GPhL/BUSTER_stable_production_20140512/autoBUSTER/grade-data/ccp4_atomtype_hybridisation.dat Adding new plane N49 C50 N54 C55 suggested by mogul Assuming molecule is uncharged Your licence will expire soon ! Today is Wed May 28 21:02:45 2014 Your licence will expire on Mon Jun 23 01:00:00 2014 Your licence will expire soon ! Today is Wed May 28 21:05:48 2014 Your licence will expire on Mon Jun 23 01:00:00 2014 Fixing up pseudochirals for MOL2 found 14 pseudochiral centre(s); marking them as 'both' Method details: "MOGUL 1.6(RC5), CSD as535be, with quantum mechanics RM1" Now running recognise-compound utilty to check whether the ligand is a known PDB chemical component. recognise-compound 880.grade_PDB_ligand.pdb results in "Input is known PDB chemical component "cyclohexyl-{4-[5-(3,4-dichlorophenyl)-2-piperidin-4-yl-3-propyl-3h-imidazol-4-yl]-pyrimidin-2-yl}amine" with three-letter code 880" Generated CIF 880.grade_PDB_ligand.cif and PDB 880.grade_PDB_ligand.pdb Use the command EditREFMAC 880.grade_PDB_ligand.cif 880.grade_PDB_ligand.pdb 880 to view and edit this dictionary (cpu secs used: 184.9 real, 177.8 user, 2.6 sys) real 3m20.402s user 3m3.951s sys 0m5.856s