********>Bugfix 4: Author: Terry Lang, Devleena Shivakumar, Scott Brozell Date: August 21, 2006 Program: dock Description: Several issues related to scoring are treated: (1) If a primary_score is called with minimization and a secondary_score is called without minimization, then the secondary_score was not being calculated. New logic has been added to catch this loophole. (2) Amber_score was not writing the final pose of the complex. It now does. (3) Amber_score could not effectively be used as a secondary_score. This function has been temporarily deprecated, and using input parameter amber_score_secondary causes program termination. The recommended protocol is to perform two DOCK runs with the second run specifying amber_score as the primary_score. Fix: make the following changes to the files src/dock/library_file.cpp, src/dock/score_amber.cpp, and various files in install/test. This is most easily performed via cd DOCK_HOME; patch -p0 < bugfix.4 ------------------------------------------------------------------------- *** src/dock/library_file.cpp 3 Aug 2006 00:46:09 -0000 1.13.2.3 --- src/dock/library_file.cpp 4 Aug 2006 00:40:36 -0000 1.13.2.4 *************** *** 956,961 **** --- 956,965 ---- score.compute_secondary_score(mol); } } + }else{ + if(!score.primary_min || !score.secondary_min){ + score.compute_secondary_score(mol); + } } } else { mol.current_score = 0.0; =================================================================== *** score_amber.cpp 23 Aug 2006 23:45:33 -0000 1.32.2.4 --- score_amber.cpp 24 Aug 2006 01:12:25 -0000 1.32.2.6 *************** *** 111,117 **** if ( !secondary_score ) { yesorno = parm.query_param ( "amber_score_secondary", "no", "yes no" ); use_secondary_score = ( yesorno == "yes" ); ! secondary_score = use_secondary_score; } use_score = ( use_primary_score || use_secondary_score ); --- 111,128 ---- if ( !secondary_score ) { yesorno = parm.query_param ( "amber_score_secondary", "no", "yes no" ); use_secondary_score = ( yesorno == "yes" ); ! // temporarily disable amber_score_secondary until next release ! if ( use_secondary_score ) { ! cout << "TEMPORARILY DEPRECATED OPTION!" ! << endl ! << " Amber score as a secondary score is disabled." ! << endl ! << " The recommended protocol is to perform two DOCK runs with" ! << endl ! << " the second run specifying amber_score as the primary_score." ! << endl; ! exit(0); ! } } use_score = ( use_primary_score || use_secondary_score ); *************** *** 505,510 **** --- 516,522 ---- restraint_atomexpr, dummy, NULL ); complex_energy = mme ( &complex_xyz[0], &gradient_xyz[0], &nab_mme_initial_iteration ); + setmol_from_xyz ( &complex, NULL, &complex_xyz[0] ); putpdb ( const_cast < char *>( complex_final_pdb.c_str ( ) ), complex, NULL ); // Print the initial energies on the screen =================================================================== *** install/test/amber_score_181l/move_ligand.dockin 24 Aug 2006 00:45:42 -0000 1.5.2.3 --- install/test/amber_score_181l/move_ligand.dockin 23 Aug 2006 23:45:30 -0000 1.5.2.2 *************** *** 25,31 **** gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 181l amber_score_movable_region ligand amber_score_gb_model 5 --- 25,31 ---- gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 181l amber_score_movable_region ligand amber_score_gb_model 5 =================================================================== *** install/test/amber_score_1a28/move_everything.dockin 24 Aug 2006 00:45:49 -0000 1.10.2.3 --- install/test/amber_score_1a28/move_everything.dockin 23 Aug 2006 23:45:31 -0000 1.10.2.2 *************** *** 25,31 **** gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1a28 amber_score_movable_region everything amber_score_gb_model 5 --- 25,31 ---- gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1a28 amber_score_movable_region everything amber_score_gb_model 5 =================================================================== *** install/test/amber_score_1lgu/move_by_atom_expression.dockin 24 Aug 2006 00:45:49 -0000 1.8.2.3 --- install/test/amber_score_1lgu/move_by_atom_expression.dockin 23 Aug 2006 23:45:31 -0000 1.8.2.2 *************** *** 25,31 **** gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1lgu amber_score_movable_region nab_atom_expression amber_score_movable_atom_expression 2::|1:102 --- 25,31 ---- gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1lgu amber_score_movable_region nab_atom_expression amber_score_movable_atom_expression 2::|1:102 =================================================================== *** install/test/amber_score_1lgu/move_everything.dockin 24 Aug 2006 00:45:49 -0000 1.13.2.3 --- install/test/amber_score_1lgu/move_everything.dockin 23 Aug 2006 23:45:31 -0000 1.13.2.2 *************** *** 25,31 **** gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1lgu amber_score_movable_region everything amber_score_gb_model 5 --- 25,31 ---- gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1lgu amber_score_movable_region everything amber_score_gb_model 5 =================================================================== *** install/test/amber_score_1lgu/move_ligand.dockin 24 Aug 2006 00:45:49 -0000 1.9.2.3 --- install/test/amber_score_1lgu/move_ligand.dockin 23 Aug 2006 23:45:31 -0000 1.9.2.2 *************** *** 25,31 **** gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1lgu amber_score_movable_region ligand amber_score_gb_model 5 --- 25,31 ---- gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1lgu amber_score_movable_region ligand amber_score_gb_model 5 =================================================================== *** install/test/amber_score_1lgu/move_nothing.dockin 24 Aug 2006 00:45:49 -0000 1.1.2.3 --- install/test/amber_score_1lgu/move_nothing.dockin 23 Aug 2006 23:45:31 -0000 1.1.2.2 *************** *** 27,33 **** gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary no amber_score_frcmod_file_for_ligands lig.frcmod amber_score_ligand_pdb lig.amber.pdb amber_score_ligand_prmtop lig.prmtop --- 27,33 ---- gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary yes amber_score_frcmod_file_for_ligands lig.frcmod amber_score_ligand_pdb lig.amber.pdb amber_score_ligand_prmtop lig.prmtop =================================================================== *** install/test/amber_score_multiple_ligands/move_ligand.dockin 24 Aug 2006 00:45:50 -0000 1.4.2.3 --- install/test/amber_score_multiple_ligands/move_ligand.dockin 23 Aug 2006 23:45:32 -0000 1.4.2.2 *************** *** 25,31 **** gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1lgu amber_score_movable_region ligand amber_score_gb_model 5 --- 25,31 ---- gbsa_hawkins_score_primary no gbsa_hawkins_score_secondary no amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1lgu amber_score_movable_region ligand amber_score_gb_model 5 =================================================================== *** install/test/amber_score_181l/move_ligand.dockout.save 24 Aug 2006 01:00:55 -0000 1.7.2.3 --- install/test/amber_score_181l/move_ligand.dockout.save 23 Aug 2006 23:45:30 -0000 1.7.2.2 *************** *** 71,77 **** Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 181l amber_score_movable_region ligand amber_score_gb_model 5 --- 71,77 ---- Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 181l amber_score_movable_region ligand amber_score_gb_model 5 *************** *** 79,87 **** amber_score_minimization_cycles 1 amber_score_nonbonded_cutoff 18.0 amber_score_temperature 300.0 - - Warning: No secondary scoring function selected. - ------------------------------------------------------------------------------------------ Initializing Library File Routines... --- 79,84 ---- *************** *** 99,105 **** ----------------------------------- Molecule: ASL ! Elapsed time: 8 seconds Anchors: 1 Orientations: 1 --- 96,102 ---- ----------------------------------- Molecule: ASL ! Elapsed time: 4 seconds Anchors: 1 Orientations: 1 *************** *** 110,113 **** 1 Molecules Processed ! Total elapsed time: 15 seconds --- 107,110 ---- 1 Molecules Processed ! Total elapsed time: 10 seconds =================================================================== *** install/test/amber_score_1a28/move_everything.dockout.save 24 Aug 2006 01:01:07 -0000 1.19.2.3 --- install/test/amber_score_1a28/move_everything.dockout.save 23 Aug 2006 23:45:31 -0000 1.19.2.2 *************** *** 71,77 **** Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1a28 amber_score_movable_region everything amber_score_gb_model 5 --- 71,77 ---- Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1a28 amber_score_movable_region everything amber_score_gb_model 5 *************** *** 79,87 **** amber_score_minimization_cycles 1 amber_score_nonbonded_cutoff 18.0 amber_score_temperature 300.0 - - Warning: No secondary scoring function selected. - ------------------------------------------------------------------------------------------ Initializing Library File Routines... --- 79,84 ---- *************** *** 92,113 **** Computing the ligand energy: ************************************** Computing the complex energy: ! Energy of the Minimized complex is -7775.81354251 Energy of the Minimized receptor is -7760.48480724 ! Energy of the Minimized Ligand is 26.5244730719 ----------------------------------- Molecule: C1 ! Elapsed time: 47 seconds Anchors: 1 Orientations: 1 Conformations: 1 ! Amber Score: -41.853207 1 Molecules Processed ! Total elapsed time: 92 seconds --- 89,110 ---- Computing the ligand energy: ************************************** Computing the complex energy: ! Energy of the Minimized complex is -7775.81862675 Energy of the Minimized receptor is -7760.48480724 ! Energy of the Minimized Ligand is 26.5186813046 ----------------------------------- Molecule: C1 ! Elapsed time: 27 seconds Anchors: 1 Orientations: 1 Conformations: 1 ! Amber Score: -41.852501 1 Molecules Processed ! Total elapsed time: 53 seconds =================================================================== *** install/test/amber_score_1lgu/move_by_atom_expression.dockout.save 24 Aug 2006 01:01:13 -0000 1.11.2.3 --- install/test/amber_score_1lgu/move_by_atom_expression.dockout.save 23 Aug 2006 23:45:31 -0000 1.11.2.2 *************** *** 71,77 **** Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1lgu amber_score_movable_region nab_atom_expression amber_score_movable_atom_expression 2::|1:102 --- 71,77 ---- Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1lgu amber_score_movable_region nab_atom_expression amber_score_movable_atom_expression 2::|1:102 *************** *** 80,88 **** amber_score_minimization_cycles 1 amber_score_nonbonded_cutoff 18.0 amber_score_temperature 300.0 - - Warning: No secondary scoring function selected. - ------------------------------------------------------------------------------------------ Initializing Library File Routines... --- 80,85 ---- *************** *** 100,106 **** ----------------------------------- Molecule: AAH ! Elapsed time: 8 seconds Anchors: 1 Orientations: 1 --- 97,103 ---- ----------------------------------- Molecule: AAH ! Elapsed time: 5 seconds Anchors: 1 Orientations: 1 *************** *** 111,114 **** 1 Molecules Processed ! Total elapsed time: 16 seconds --- 108,111 ---- 1 Molecules Processed ! Total elapsed time: 10 seconds =================================================================== *** install/test/amber_score_1lgu/move_everything.dockout.save 24 Aug 2006 01:01:13 -0000 1.18.2.3 --- install/test/amber_score_1lgu/move_everything.dockout.save 23 Aug 2006 23:45:31 -0000 1.18.2.2 *************** *** 71,77 **** Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1lgu amber_score_movable_region everything amber_score_gb_model 5 --- 71,77 ---- Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1lgu amber_score_movable_region everything amber_score_gb_model 5 *************** *** 79,87 **** amber_score_minimization_cycles 1 amber_score_nonbonded_cutoff 18.0 amber_score_temperature 300.0 - - Warning: No secondary scoring function selected. - ------------------------------------------------------------------------------------------ Initializing Library File Routines... --- 79,84 ---- *************** *** 99,105 **** ----------------------------------- Molecule: AAH ! Elapsed time: 22 seconds Anchors: 1 Orientations: 1 --- 96,102 ---- ----------------------------------- Molecule: AAH ! Elapsed time: 13 seconds Anchors: 1 Orientations: 1 *************** *** 110,113 **** 1 Molecules Processed ! Total elapsed time: 44 seconds --- 107,110 ---- 1 Molecules Processed ! Total elapsed time: 25 seconds =================================================================== *** install/test/amber_score_1lgu/move_ligand.dockout.save 24 Aug 2006 01:01:13 -0000 1.11.2.3 --- install/test/amber_score_1lgu/move_ligand.dockout.save 23 Aug 2006 23:45:31 -0000 1.11.2.2 *************** *** 71,77 **** Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary no receptor_file_prefix 1lgu amber_score_movable_region ligand amber_score_gb_model 5 --- 71,77 ---- Amber Score Parameters ------------------------------------------------------------------------------------------ amber_score_primary yes ! amber_score_secondary yes receptor_file_prefix 1lgu amber_score_movable_region ligand amber_score_gb_model 5 *************** *** 79,87 **** amber_score_minimization_cycles 1 amber_score_nonbonded_cutoff 18.0 amber_score_temperature 300.0 - - Warning: No secondary scoring function selected. - ------------------------------------------------------------------------------------------ Initializing Library File Routines... --- 79,84 ---- *************** *** 99,105 **** ----------------------------------- Molecule: AAH ! Elapsed time: 8 seconds Anchors: 1 Orientations: 1 --- 96,102 ---- ----------------------------------- Molecule: AAH ! Elapsed time: 5 seconds Anchors: 1 Orientations: 1 *************** *** 110,113 **** 1 Molecules Processed ! Total elapsed time: 15 seconds --- 107,110 ---- 1 Molecules Processed ! Total elapsed time: 9 seconds -------------------------------------------------------------------------- Workaround: none.