[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.
More information about the Dock-fans
mailing list