[Dock-fans] 6.2 bugfix 3

Scott Brozell sbrozell at scripps.edu
Tue Nov 18 22:14:33 PST 2008


http://dock.compbio.ucsf.edu/DOCK_6/bugfixes62/6.2_bugfixes.htm

********>Bugfix 3:
Author:  Scott Brozell
Date:  Nov 18, 2008

Program:  dock.pbsa

Description:  the PB/SA score PB component was in the OpenEye energy
units of kT as opposed to the DOCK energy units of kcal/mol.
This bug exists in all previous versions of PB/SA score.
There are also small changes in the SA component that are due to
differences in the significant figures of the old vs new conversion
factors: 0.025 vs 0.0423 * 0.5961 = AREA_TO_ENERGY * kT_to_kcal/mol.

Fix:  make the following changes, most simply accomplished with the command
cd $DOCK_HOME; patch -N -p0 < bugfix.3
to the files:
install/test/pbsa_score/Makefile
install/test/pbsa_score/flexible.dockpbsaout.save
install/test/pbsa_score/flexible_scored.mol2.save
install/test/pbsa_score/pbsa1.dockpbsaout.save
install/test/pbsa_score/pbsa1_scored.mol2.save
install/test/pbsa_score/pbsa2.dockpbsaout.save
install/test/pbsa_score/pbsa2_secondary_scored.mol2.save
src/dock/score_solvent.cpp
install/test/pbsa_score/benzene.mol2
-------------------------------------------------------------------------
*** install/test/pbsa_score/Makefile	4 Feb 2008 21:48:36 -0000	1.7
--- install/test/pbsa_score/Makefile	19 Nov 2008 02:13:26 -0000
***************
*** 18,22 ****
  
  clean: clean_dock
  	/bin/rm -f pbsa1*mol2 pbsa2*mol2
! 	/bin/rm -f pbsa1.dockpbsaout pbsa2.dockpbsaout
  
--- 18,22 ----
  
  clean: clean_dock
  	/bin/rm -f pbsa1*mol2 pbsa2*mol2
! 	/bin/rm -f pbsa1.dockpbsaout pbsa2.dockpbsaout flexible.dockpbsaout
  
===================================================================
*** install/test/pbsa_score/flexible.dockpbsaout.save	4 Feb 2008 21:21:39 -0000	1.3
--- install/test/pbsa_score/flexible.dockpbsaout.save	19 Nov 2008 02:13:26 -0000
***************
*** 2,10 ****
  
  
  --------------------------------------
! DOCK v6.2dev
  
! Released Unreleased
  Copyright UCSF
  --------------------------------------
  
--- 2,10 ----
  
  
  --------------------------------------
! DOCK v6.2
  
! Released March 2008
  Copyright UCSF
  --------------------------------------
  
***************
*** 123,139 ****
  -----------------------------------
  Molecule: ADA 
  
!  Elapsed time for docking:	29 seconds
  
   Anchors:		1
   Orientations:		5
   Conformations:		2
  
!    PB/SA Score:          -14.715830
             vdw:           -8.612719
!             pb:            2.681000
!             sa:           -8.784111
  
  
  1 Molecules Processed
! Total elapsed time:	33 seconds
--- 123,139 ----
  -----------------------------------
  Molecule: ADA 
  
!  Elapsed time for docking:	24 seconds
  
   Anchors:		1
   Orientations:		5
   Conformations:		2
  
!    PB/SA Score:          -15.874229
             vdw:           -8.612719
!             pb:            1.598144
!             sa:           -8.859654
  
  
  1 Molecules Processed
! Total elapsed time:	28 seconds
===================================================================
*** install/test/pbsa_score/flexible_scored.mol2.save	4 Feb 2008 21:49:41 -0000	1.1
--- install/test/pbsa_score/flexible_scored.mol2.save	19 Nov 2008 02:13:26 -0000
***************
*** 1,9 ****
  
  ########## Name:		ADA 
! ##########   PB/SA Score:          -14.715830
  ##########           vdw:           -8.612719
! ##########            pb:            2.681000
! ##########            sa:           -8.784111
  
  @<TRIPOS>MOLECULE
  ADA 
--- 1,9 ----
  
  ########## Name:		ADA 
! ##########   PB/SA Score:          -15.874229
  ##########           vdw:           -8.612719
! ##########            pb:            1.598144
! ##########            sa:           -8.859654
  
  @<TRIPOS>MOLECULE
  ADA 
===================================================================
*** install/test/pbsa_score/pbsa1.dockpbsaout.save	4 Mar 2008 03:34:10 -0000	1.14
--- install/test/pbsa_score/pbsa1.dockpbsaout.save	19 Nov 2008 02:13:26 -0000
***************
*** 112,122 ****
   Orientations:		1
   Conformations:		1
  
!    PB/SA Score:          -37.486446
!            vdw:          -32.735348
!             pb:           13.194916
!             sa:          -17.946014
  
  
  1 Molecules Processed
! Total elapsed time:	7 seconds
--- 112,122 ----
   Orientations:		1
   Conformations:		1
  
!    PB/SA Score:          -42.970211
!            vdw:          -32.735352
!             pb:            7.865489
!             sa:          -18.100349
  
  
  1 Molecules Processed
! Total elapsed time:	6 seconds
===================================================================
*** install/test/pbsa_score/pbsa1_scored.mol2.save	17 Nov 2006 04:52:12 -0000	1.2
--- install/test/pbsa_score/pbsa1_scored.mol2.save	19 Nov 2008 02:13:26 -0000
***************
*** 1,9 ****
  
  ########## Name:		 C1 
! ##########   PB/SA Score:          -37.486450
  ##########           vdw:          -32.735352
! ##########            pb:           13.194916
! ##########            sa:          -17.946014
  
  @<TRIPOS>MOLECULE
   C1 
--- 1,9 ----
  
  ########## Name:		 C1 
! ##########   PB/SA Score:          -42.970211
  ##########           vdw:          -32.735352
! ##########            pb:            7.865489
! ##########            sa:          -18.100349
  
  @<TRIPOS>MOLECULE
   C1 
===================================================================
*** install/test/pbsa_score/pbsa2.dockpbsaout.save	4 Mar 2008 03:34:11 -0000	1.15
--- install/test/pbsa_score/pbsa2.dockpbsaout.save	19 Nov 2008 02:13:26 -0000
***************
*** 113,119 ****
  
   Anchors:		1
   Orientations:		50
!  Conformations:		49
  
   Primary Score
   Contact Score:          -35.000000
--- 113,119 ----
  
   Anchors:		1
   Orientations:		50
!  Conformations:		50
  
   Primary Score
   Contact Score:          -35.000000
***************
*** 125,153 ****
  
   Anchors:		1
   Orientations:		50
!  Conformations:		46
  
   Primary Score
!  Contact Score:          -46.000000
  
  -----------------------------------
  Molecule: ZINC00158751
  
   Secondary Score
!    PB/SA Score:          -10.401018
!            vdw:           -6.890557
!             pb:            5.476242
!             sa:           -8.986703
  
  -----------------------------------
  Molecule: ZINC00013564
  
   Secondary Score
!    PB/SA Score:        23023.501953
!            vdw:        23025.291016
!             pb:            8.534439
!             sa:          -10.323522
  
  
  2 Molecules Processed
! Total elapsed time:	10 seconds
--- 125,153 ----
  
   Anchors:		1
   Orientations:		50
!  Conformations:		48
  
   Primary Score
!  Contact Score:          -28.000000
  
  -----------------------------------
  Molecule: ZINC00158751
  
   Secondary Score
!    PB/SA Score:          -12.690160
!            vdw:           -6.890559
!             pb:            3.264388
!             sa:           -9.063989
  
  -----------------------------------
  Molecule: ZINC00013564
  
   Secondary Score
!    PB/SA Score:          -17.994326
!            vdw:           -9.296841
!             pb:            2.826463
!             sa:          -11.523949
  
  
  2 Molecules Processed
! Total elapsed time:	8 seconds
===================================================================
*** install/test/pbsa_score/pbsa2_secondary_scored.mol2.save	22 Nov 2006 23:01:11 -0000	1.1
--- install/test/pbsa_score/pbsa2_secondary_scored.mol2.save	19 Nov 2008 02:13:26 -0000
***************
*** 1,10 ****
  
  ########## Name:		ZINC00158751
  ########## SECONDARY SCORE
! ##########   PB/SA Score:          -10.401020
  ##########           vdw:           -6.890559
! ##########            pb:            5.476242
! ##########            sa:           -8.986703
  ########## PRIMARY SCORE
  ########## Contact Score:          -35.000000
  
--- 1,10 ----
  
  ########## Name:		ZINC00158751
  ########## SECONDARY SCORE
! ##########   PB/SA Score:          -12.690160
  ##########           vdw:           -6.890559
! ##########            pb:            3.264388
! ##########            sa:           -9.063989
  ########## PRIMARY SCORE
  ########## Contact Score:          -35.000000
  
***************
*** 45,54 ****
  
  ########## Name:		ZINC00013564
  ########## SECONDARY SCORE
! ##########   PB/SA Score:          -15.980936
  ##########           vdw:           -9.296841
! ##########            pb:            4.741592
! ##########            sa:          -11.425688
  ########## PRIMARY SCORE
  ########## Contact Score:          -28.000000
  
--- 45,54 ----
  
  ########## Name:		ZINC00013564
  ########## SECONDARY SCORE
! ##########   PB/SA Score:          -17.994326
  ##########           vdw:           -9.296841
! ##########            pb:            2.826463
! ##########            sa:          -11.523949
  ########## PRIMARY SCORE
  ########## Contact Score:          -28.000000
  
===================================================================
*** src/dock/score_solvent.cpp	20 Mar 2007 02:13:44 -0000	1.35
--- src/dock/score_solvent.cpp	19 Nov 2008 02:13:27 -0000
***************
*** 1,3 ****
--- 1,4 ----
+ #include <time.h>
  #include <iomanip>
  #include <iostream>
  #include <sstream>
***************
*** 1903,1919 ****
          }
  
          if (verbose) {
!             cout << "LIGAND\t PB=" << 0.5 * lig_solv << "\tSA=" << 0.025 *
                  lig_area << endl;
!             cout << "RECEPTOR PB=" << 0.5 * prot_solv << "\tSA=" << 0.025 *
                  prot_area << endl;
!             cout << "COMPLEX\t PB=" << 0.5 * comp_solv << "\tSA=" << 0.025 *
                  comp_area << endl;
          }
  
!         pb_component = (0.5 * comp_solv) - (0.5 * lig_solv) - (0.5 * prot_solv);
          sa_component =
!             (0.025 * comp_area) - (0.025 * lig_area) - (0.025 * prot_area);
  
          mol.current_score = vdw_component + pb_component + sa_component;
          mol.current_data = output_score_summary(mol.current_score);
--- 1904,1920 ----
          }
  
          if (verbose) {
!             cout << "LIGAND\t PB=" << 0.29805 * lig_solv << "\tSA=" << 0.025215 *
                  lig_area << endl;
!             cout << "RECEPTOR PB=" << 0.29805 * prot_solv << "\tSA=" << 0.025215 *
                  prot_area << endl;
!             cout << "COMPLEX\t PB=" << 0.29805 * comp_solv << "\tSA=" << 0.025215 *
                  comp_area << endl;
          }
  
!         pb_component = 0.29805 * (comp_solv - lig_solv - prot_solv);
          sa_component =
!             0.025215 * (comp_area - lig_area - prot_area);
  
          mol.current_score = vdw_component + pb_component + sa_component;
          mol.current_data = output_score_summary(mol.current_score);
===================================================================
--- /dev/null	2004-06-24 14:04:38.000000000 -0400
+++ install/test/pbsa_score/benzene.mol2	2008-10-02 01:10:15.000000000 -0400
@@ -0,0 +1,35 @@
+@<TRIPOS>MOLECULE
+ADA 
+   12    12     1     0     0
+SMALL
+bcc
+
+
+@<TRIPOS>ATOM
+      1 C1         26.7300    6.5760    6.0730 C.ar      1 ADA     -0.130100
+      2 C2         25.8430    5.5400    5.7540 C.ar      1 ADA     -0.130000
+      3 C3         27.5490    7.1270    5.0800 C.ar      1 ADA     -0.130200
+      4 C4         25.7750    5.0570    4.4400 C.ar      1 ADA     -0.130200
+      5 C5         27.4810    6.6440    3.7670 C.ar      1 ADA     -0.130100
+      6 C6         26.5940    5.6080    3.4480 C.ar      1 ADA     -0.130100
+      7 H7         26.7820    6.9420    7.0670 H         1 ADA      0.130200
+      8 H8         25.2230    5.1210    6.5060 H         1 ADA      0.130300
+      9 H9         28.2210    7.9120    5.3220 H         1 ADA      0.130000
+     10 H10        25.1040    4.2710    4.1990 H         1 ADA      0.130000
+     11 H11        28.1020    7.0620    3.0150 H         1 ADA      0.130200
+     12 H12        26.5430    5.2410    2.4530 H         1 ADA      0.130100
+@<TRIPOS>BOND
+     1    1    2 ar  
+     2    1    3 ar  
+     3    1    7 1   
+     4    2    4 ar  
+     5    2    8 1   
+     6    3    5 ar  
+     7    3    9 1   
+     8    4    6 ar  
+     9    4   10 1   
+    10    5    6 ar  
+    11    5   11 1   
+    12    6   12 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 ADA         1 TEMP              0 ****  ****    0 ROOT
--------------------------------------------------------------------------

Workaround:  none.




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