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Commit 558a3418 authored by Leonardo Solis's avatar Leonardo Solis
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add fpga build in Makefile + init_aoc_esa.sh

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.gitignore
View file @ 558a3418
......@@ -2,7 +2,15 @@
PDBs/*
ofdock_taskpar_alt/Krnl_GA/*
ofdock_taskpar_alt/device/docking_fpga_leo/*
# Ignore FPGA binaries
ofdock_taskpar_alt/docking/*
ofdock_taskpar_alt/docking.aoco
ofdock_taskpar_alt/docking.aocx
# Ignore docking debug/tmp output
*~
final_population_run*
# ===================
# C gitignore
......
README.md
View file @ 558a3418
Version compiled with Intel Altera Tools 16.1
Source first: init_aoc_esa.sh
ofdock_datapar_xl: data parallel version for altera taken from feanor
Machine: feanor
Path: /home/wimi/lvs/altera/ofdock_altera/ofdock
ofdock_taskpar_xl: task parallel version for altera
ofdock_taskpar_alt/Makefile
View file @ 558a3418
......@@ -199,7 +199,6 @@ else
REP=
endif
# =============================
......@@ -220,38 +219,89 @@ $(TARGET_DIR)/$(TARGET) : Makefile $(SRCS) $(INCS) $(TARGET_DIR)
$(foreach D,$(LIB_DIRS),-L$D) \
$(foreach L,$(LIBS),-l$L) \
-o $(TARGET_DIR)/$(TARGET) $(DOCK_DEBUG_FLAG) $(DEV) $(DOCK_PROG) $(ENABLE_KERNELS) $(REP)
@echo " "
@echo "================================"
@echo "INFO: host binary is under: bin/"
@echo "================================"
@echo " "
# Docking parameters
PDB := 1stp
NRUN := 10
NEV := 200000
PDB := 3ptb
NRUN := 20
NEV := 300000
# Make it all: compilation (host & device) + run
# Notice, it switches automatically to /bin folder
emu: $(TARGET_DIR)/$(TARGET) keremu runemu
# Device folder
# Device main kernel name
# Device main kernel source
DEV_DIRS := device
DEV_SRC := $(DEV_DIRS)/Krnl_GA.cl
## Make it all: compilation (host & device) + run emulation
## Notice, it switches automatically to /bin folder
#emu: $(TARGET_DIR)/$(TARGET) keremu runemu
# Build kernel binary only for emulation
# Creates under bin:
# "docking" folder
# docking.aoco
# docking.aocx
keremu: $(DEV_SRC)
aoc -march=emulator -v --board a10gx $(DEV_SRC) -o $(TARGET_DIR)/docking.aocx $(REP)
runemu: $(TARGET)
@echo " "
@echo "=========================================================="
@echo "INFO: emulation files are under: bin/docking(.aoco)(.aocx)"
@echo "=========================================================="
@echo " "
# Run emulation
# Compilation (host & device) if not done previously
# The working directory is changed
# So .dlg file is written there
emu: $(TARGET_DIR)/$(TARGET) keremu
cd $(TARGET_DIR) && \
CL_CONTEXT_EMULATOR_DEVICE_ALTERA=1 ./$(TARGET) -ffile ../input/$(PDB)/derived/$(PDB)_protein.maps.fld -lfile ../input/$(PDB)/derived/$(PDB)_ligand.pdbqt -nev $(NEV) -nrun $(NRUN) -gfpop 1
@echo " "
@echo "========================================"
@echo "INFO: log file is under: bin/docking.dlg"
@echo "========================================"
@echo " "
# Reports are generated
# Could be used in multistep compilation
# Creates under bin:
# "docking" folder -> /reports/report.html, to see details
# docking.aoco
# No actual hardware is built (NO .aocx)
kerrpt: $(DEV_SRC)
aoc --board a10gx $(DEV_SRC) -o $(TARGET_DIR)/docking.aoco $(REP) -c --report
@echo " "
@echo "============================================================="
@echo "INFO: report files are under: bin/docking/reports/report.html"
@echo "============================================================="
@echo " "
# Build hw (FPGA bitstream)
# NOT integrated yet in a multistep compilation
# Creates under root folder:
# "docking" folder
# docking.aoco
# docking.aocx
hw:
aoc --board a10gx $(DEV_SRC) -o docking.aocx
@echo " "
@echo "================================="
@echo "INFO: FPGA bitstream is under: ./"
@echo "================================="
@echo " "
# CL_CONTEXT_EMULATOR_DEVICE_ALTERA=1 ./$(TARGET) -ffile ../input/3ptb/derived/3ptb_protein.maps.fld -lfile ../input/3ptb/derived/3ptb_ligand.pdbqt -nev 250000 -nrun 40
$(TARGET_DIR) :
$(ECHO)mkdir $(TARGET_DIR)
......
ofdock_taskpar_alt/bin/docking.dlg deleted 100644 → 0
View file @ ee1ce9a3
**********************************************************
** GDOCK AUTODOCKTOOLS-COMPATIBLE DLG FILE **
**********************************************************
DOCKING PARAMETERS
________________________
Ligand file: ../input_data/3ptb/derived/3ptb_ligand.pdbqt
Grid fld file: ../input_data/3ptb/derived/3ptb_protein.maps.fld
Number of runs: 40
Number of energy evaluations: 100011
Number of generations: 670
Size of population: 150
Rate of crossover: 80.000000%
Tournament selection probability limit: 60.000000%
Rate of mutation: 2.000000%
Maximal allowed delta movement: +/- 6.000000A
Maximal allowed delta angle: +/- 90.000000
Rate of local search: 6.000000%
Maximal number of local search iterations: 300
Rho lower bound: 0.010000
Spread of local search delta movement: 2.000000A
Spread of local search delta angle: 74.999999
Limit of consecutive successes/failures: 4
Handle symmetry during clustering: NO
RMSD tolerance: 2.000000A
Program call in command line was: ./host -ffile ../input_data/3ptb/derived/3ptb_protein.maps.fld -lfile ../input_data/3ptb/derived/3ptb_ligand.pdbqt -nev 100000 -nrun 40
GRID PARAMETERS
________________________
Receptor name: 3ptb_protein
Number of grid points (x, y, z): 7, 13, 17
Grid size (x, y, z): 2.250000, 4.500000, 6.000000A
Grid spacing: 0.375000A
LIGAND PARAMETERS
________________________
Ligand name: ../input_data/3ptb/derived/3ptb_ligand
Number of atoms: 13
Number of rotatable bonds: 2
Number of atom types: 4
DUMMY DATA (only for ADT-compatibility)
________________________
DPF> outlev 1
DPF> ga_run 40
DPF> fld 3ptb_protein.maps.fld
DPF> move ../input_data/3ptb/derived/3ptb_ligand.pdbqt
INPUT LIGAND PDBQT FILE:
________________________
INPUT-LIGAND-PDBQT: REMARK 2 active torsions:
INPUT-LIGAND-PDBQT: REMARK status: ('A' for Active; 'I' for Inactive)
INPUT-LIGAND-PDBQT: REMARK 1 A between atoms: C1_1 and C_7
INPUT-LIGAND-PDBQT: REMARK 2 A between atoms: C_7 and N1_8
INPUT-LIGAND-PDBQT: ROOT
INPUT-LIGAND-PDBQT: HETATM 1 C1 BEN A 1 -1.853 14.311 16.658 1.00 19.86 0.007 A
INPUT-LIGAND-PDBQT: HETATM 2 C2 BEN A 1 -2.107 15.653 16.758 1.00 19.86 0.015 A
INPUT-LIGAND-PDBQT: HETATM 3 C3 BEN A 1 -1.774 16.341 17.932 1.00 19.86 0.001 A
INPUT-LIGAND-PDBQT: HETATM 4 C4 BEN A 1 -1.175 15.662 19.005 1.00 19.86 0.000 A
INPUT-LIGAND-PDBQT: HETATM 5 C5 BEN A 1 -0.914 14.295 18.885 1.00 19.86 0.001 A
INPUT-LIGAND-PDBQT: HETATM 6 C6 BEN A 1 -1.257 13.634 17.708 1.00 19.86 0.015 A
INPUT-LIGAND-PDBQT: ENDROOT
INPUT-LIGAND-PDBQT: BRANCH 1 7
INPUT-LIGAND-PDBQT: HETATM 7 C BEN A 1 -2.193 13.627 15.496 1.00 19.86 0.102 C
INPUT-LIGAND-PDBQT: HETATM 8 N2 BEN A 1 -1.762 12.391 15.309 1.00 19.86 -0.385 N
INPUT-LIGAND-PDBQT: HETATM 9 H22 BEN A 1 -1.296 11.921 16.085 1.00 0.00 0.157 HD
INPUT-LIGAND-PDBQT: HETATM 10 H21 BEN A 1 -2.011 11.889 14.457 1.00 0.00 0.157 HD
INPUT-LIGAND-PDBQT: BRANCH 7 11
INPUT-LIGAND-PDBQT: HETATM 11 N1 BEN A 1 -2.797 14.235 14.491 1.00 19.86 -0.385 N
INPUT-LIGAND-PDBQT: HETATM 12 H12 BEN A 1 -3.129 15.188 14.635 1.00 0.00 0.157 HD
INPUT-LIGAND-PDBQT: HETATM 13 H11 BEN A 1 -3.046 13.733 13.639 1.00 0.00 0.157 HD
INPUT-LIGAND-PDBQT: ENDBRANCH 7 11
INPUT-LIGAND-PDBQT: ENDBRANCH 1 7
INPUT-LIGAND-PDBQT: TORSDOF 2
FINAL DOCKED STATE:
________________________
Run: 1 / 40
Time taken for this run: 98.703s
DOCKED: MODEL 1
DOCKED: USER Run = 1
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = +1.29 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = +0.69 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = +0.71 kcal/mol
DOCKED: USER Electrostatic Energy = -0.02 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = +0.17 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +0.60 kcal/mol
DOCKED: USER (4) Unbound System's Energy = +0.17 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK 2 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C1_1 and C_7
DOCKED: REMARK 2 A between atoms: C_7 and N1_8
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: HETATM 1 C1 BEN A 1 -1.735 14.226 16.176 -0.60 -0.00 +0.007 A
DOCKED: HETATM 2 C2 BEN A 1 -1.767 15.348 15.391 -0.05 -0.01 +0.015 A
DOCKED: HETATM 3 C3 BEN A 1 -2.012 15.232 14.017 +1.84 -0.00 +0.001 A
DOCKED: HETATM 4 C4 BEN A 1 -2.231 13.970 13.441 -0.34 -0.00 +0.000 A
DOCKED: HETATM 5 C5 BEN A 1 -2.204 12.836 14.255 +1.03 -0.00 +0.001 A
DOCKED: HETATM 6 C6 BEN A 1 -1.956 12.979 15.618 -0.64 -0.01 +0.015 A
DOCKED: ENDROOT
DOCKED: BRANCH 1 7
DOCKED: HETATM 7 C BEN A 1 -1.482 14.342 17.538 -0.65 -0.03 +0.102 C
DOCKED: HETATM 8 N2 BEN A 1 -1.118 13.278 18.233 -0.63 +0.10 -0.385 N
DOCKED: HETATM 9 H22 BEN A 1 -0.904 12.420 17.724 -0.14 -0.05 +0.157 HD
DOCKED: HETATM 10 H21 BEN A 1 -0.932 13.362 19.233 -0.02 -0.03 +0.157 HD
DOCKED: BRANCH 7 11
DOCKED: HETATM 11 N1 BEN A 1 -1.758 15.452 18.198 -0.51 +0.06 -0.385 N
DOCKED: HETATM 12 H12 BEN A 1 -0.993 15.936 18.667 -0.00 -0.02 +0.157 HD
DOCKED: HETATM 13 H11 BEN A 1 -2.720 15.754 18.351 -0.04 -0.02 +0.157 HD
DOCKED: ENDBRANCH 7 11
DOCKED: ENDBRANCH 1 7
DOCKED: TORSDOF 2
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
FINAL DOCKED STATE:
________________________
Run: 2 / 40
Time taken for this run: 98.703s
DOCKED: MODEL 2
DOCKED: USER Run = 2
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -5.43 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -6.03 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -5.92 kcal/mol
DOCKED: USER Electrostatic Energy = -0.10 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = +0.19 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +0.60 kcal/mol
DOCKED: USER (4) Unbound System's Energy = +0.19 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK 2 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C1_1 and C_7
DOCKED: REMARK 2 A between atoms: C_7 and N1_8
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: HETATM 1 C1 BEN A 1 -1.931 14.233 16.479 -0.60 -0.00 +0.007 A
DOCKED: HETATM 2 C2 BEN A 1 -2.572 15.413 16.747 -0.59 -0.01 +0.015 A
DOCKED: HETATM 3 C3 BEN A 1 -2.384 16.044 17.984 -0.49 -0.00 +0.001 A
DOCKED: HETATM 4 C4 BEN A 1 -1.536 15.475 18.947 -0.50 -0.00 +0.000 A
DOCKED: HETATM 5 C5 BEN A 1 -0.882 14.276 18.656 -0.59 -0.00 +0.001 A
DOCKED: HETATM 6 C6 BEN A 1 -1.088 13.668 17.420 -0.60 -0.00 +0.015 A
DOCKED: ENDROOT
DOCKED: BRANCH 1 7
DOCKED: HETATM 7 C BEN A 1 -2.126 13.602 15.255 -0.75 -0.10 +0.102 C
DOCKED: HETATM 8 N2 BEN A 1 -2.624 14.282 14.236 -0.69 +0.45 -0.385 N
DOCKED: HETATM 9 H22 BEN A 1 -2.732 15.291 14.336 -0.59 -0.16 +0.157 HD
DOCKED: HETATM 10 H21 BEN A 1 -2.767 13.820 13.338 -0.50 -0.31 +0.157 HD
DOCKED: BRANCH 7 11
DOCKED: HETATM 11 N1 BEN A 1 -1.986 12.296 15.124 -0.57 +0.57 -0.385 N
DOCKED: HETATM 12 H12 BEN A 1 -1.990 11.724 15.968 -0.61 -0.21 +0.157 HD
DOCKED: HETATM 13 H11 BEN A 1 -1.748 11.874 14.226 -0.49 -0.33 +0.157 HD
DOCKED: ENDBRANCH 7 11
DOCKED: ENDBRANCH 1 7
DOCKED: TORSDOF 2
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
FINAL DOCKED STATE:
________________________
Run: 3 / 40
Time taken for this run: 98.703s
DOCKED: MODEL 3
DOCKED: USER Run = 3
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -1.07 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -1.67 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -1.63 kcal/mol
DOCKED: USER Electrostatic Energy = -0.04 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = +0.17 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +0.60 kcal/mol
DOCKED: USER (4) Unbound System's Energy = +0.17 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK 2 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C1_1 and C_7
DOCKED: REMARK 2 A between atoms: C_7 and N1_8
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: HETATM 1 C1 BEN A 1 -1.956 14.143 16.000 -0.63 -0.00 +0.007 A
DOCKED: HETATM 2 C2 BEN A 1 -2.333 15.130 15.129 -0.36 -0.01 +0.015 A
DOCKED: HETATM 3 C3 BEN A 1 -2.358 14.875 13.752 +0.16 -0.00 +0.001 A
DOCKED: HETATM 4 C4 BEN A 1 -2.003 13.609 13.260 -0.21 -0.00 +0.000 A
DOCKED: HETATM 5 C5 BEN A 1 -1.628 12.609 14.161 +0.83 -0.00 +0.001 A
DOCKED: HETATM 6 C6 BEN A 1 -1.610 12.890 15.525 -0.67 -0.01 +0.015 A
DOCKED: ENDROOT
DOCKED: BRANCH 1 7
DOCKED: HETATM 7 C BEN A 1 -1.922 14.401 17.366 -0.65 -0.03 +0.102 C
DOCKED: HETATM 8 N2 BEN A 1 -2.001 13.400 18.227 -0.62 +0.11 -0.385 N
DOCKED: HETATM 9 H22 BEN A 1 -1.953 12.448 17.865 -0.26 -0.07 +0.157 HD
DOCKED: HETATM 10 H21 BEN A 1 -1.976 13.589 19.229 -0.08 -0.04 +0.157 HD
DOCKED: BRANCH 7 11
DOCKED: HETATM 11 N1 BEN A 1 -1.983 15.633 17.836 -0.52 +0.07 -0.385 N
DOCKED: HETATM 12 H12 BEN A 1 -1.126 16.056 18.190 -0.00 -0.02 +0.157 HD
DOCKED: HETATM 13 H11 BEN A 1 -2.876 16.108 17.967 -0.08 -0.03 +0.157 HD
DOCKED: ENDBRANCH 7 11
DOCKED: ENDBRANCH 1 7
DOCKED: TORSDOF 2
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
FINAL DOCKED STATE:
________________________
Run: 4 / 40
Time taken for this run: 98.703s
DOCKED: MODEL 4
DOCKED: USER Run = 4
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -5.47 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -6.07 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -5.95 kcal/mol
DOCKED: USER Electrostatic Energy = -0.12 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = +0.25 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +0.60 kcal/mol
DOCKED: USER (4) Unbound System's Energy = +0.25 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK 2 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C1_1 and C_7
DOCKED: REMARK 2 A between atoms: C_7 and N1_8
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: HETATM 1 C1 BEN A 1 -1.909 14.242 16.532 -0.60 -0.00 +0.007 A
DOCKED: HETATM 2 C2 BEN A 1 -2.431 15.503 16.650 -0.58 -0.01 +0.015 A
DOCKED: HETATM 3 C3 BEN A 1 -2.270 16.216 17.845 -0.49 -0.00 +0.001 A
DOCKED: HETATM 4 C4 BEN A 1 -1.569 15.648 18.920 -0.49 -0.00 +0.000 A
DOCKED: HETATM 5 C5 BEN A 1 -1.034 14.364 18.782 -0.58 -0.00 +0.001 A
DOCKED: HETATM 6 C6 BEN A 1 -1.211 13.675 17.585 -0.61 -0.00 +0.015 A
DOCKED: ENDROOT
DOCKED: BRANCH 1 7
DOCKED: HETATM 7 C BEN A 1 -2.079 13.531 15.349 -0.75 -0.09 +0.102 C
DOCKED: HETATM 8 N2 BEN A 1 -2.628 14.118 14.300 -0.69 +0.47 -0.385 N
DOCKED: HETATM 9 H22 BEN A 1 -2.796 15.124 14.344 -0.60 -0.16 +0.157 HD
DOCKED: HETATM 10 H21 BEN A 1 -2.753 13.597 13.432 -0.51 -0.35 +0.157 HD
DOCKED: BRANCH 7 11
DOCKED: HETATM 11 N1 BEN A 1 -1.862 12.229 15.292 -0.63 +0.52 -0.385 N
DOCKED: HETATM 12 H12 BEN A 1 -1.722 11.726 16.167 -0.59 -0.19 +0.157 HD
DOCKED: HETATM 13 H11 BEN A 1 -1.705 11.756 14.402 -0.50 -0.32 +0.157 HD
DOCKED: ENDBRANCH 7 11
DOCKED: ENDBRANCH 1 7
DOCKED: TORSDOF 2
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
FINAL DOCKED STATE:
________________________
Run: 5 / 40
Time taken for this run: 98.703s
DOCKED: MODEL 5
DOCKED: USER Run = 5
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -4.31 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -4.90 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -4.81 kcal/mol
DOCKED: USER Electrostatic Energy = -0.09 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = +0.17 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +0.60 kcal/mol
DOCKED: USER (4) Unbound System's Energy = +0.17 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK 2 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C1_1 and C_7
DOCKED: REMARK 2 A between atoms: C_7 and N1_8
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: HETATM 1 C1 BEN A 1 -1.699 14.052 16.502 -0.60 -0.00 +0.007 A
DOCKED: HETATM 2 C2 BEN A 1 -1.945 12.956 17.285 -0.45 -0.01 +0.015 A
DOCKED: HETATM 3 C3 BEN A 1 -1.656 12.998 18.655 -0.42 -0.00 +0.001 A
DOCKED: HETATM 4 C4 BEN A 1 -1.121 14.161 19.231 -0.60 -0.00 +0.000 A
DOCKED: HETATM 5 C5 BEN A 1 -0.883 15.274 18.422 -0.51 -0.00 +0.001 A
DOCKED: HETATM 6 C6 BEN A 1 -1.177 15.206 17.062 -0.45 -0.00 +0.015 A
DOCKED: ENDROOT
DOCKED: BRANCH 1 7
DOCKED: HETATM 7 C BEN A 1 -1.976 14.007 15.140 -0.74 -0.08 +0.102 C
DOCKED: HETATM 8 N2 BEN A 1 -2.392 15.095 14.516 -0.37 +0.31 -0.385 N
DOCKED: HETATM 9 H22 BEN A 1 -2.374 15.979 15.025 -0.52 -0.11 +0.157 HD
DOCKED: HETATM 10 H21 BEN A 1 -2.596 15.062 13.517 -0.48 -0.16 +0.157 HD
DOCKED: BRANCH 7 11
DOCKED: HETATM 11 N1 BEN A 1 -1.999 12.863 14.480 -0.61 +0.59 -0.385 N
DOCKED: HETATM 12 H12 BEN A 1 -1.503 12.067 14.880 -0.18 -0.21 +0.157 HD
DOCKED: HETATM 13 H11 BEN A 1 -2.384 12.801 13.538 -0.51 -0.41 +0.157 HD
DOCKED: ENDBRANCH 7 11
DOCKED: ENDBRANCH 1 7
DOCKED: TORSDOF 2
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
FINAL DOCKED STATE:
________________________
Run: 6 / 40
Time taken for this run: 98.703s
DOCKED: MODEL 6
DOCKED: USER Run = 6
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -0.56 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -1.16 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -1.16 kcal/mol
DOCKED: USER Electrostatic Energy = +0.00 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = +0.19 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +0.60 kcal/mol
DOCKED: USER (4) Unbound System's Energy = +0.19 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK 2 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C1_1 and C_7
DOCKED: REMARK 2 A between atoms: C_7 and N1_8
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: HETATM 1 C1 BEN A 1 -2.006 13.672 16.015 -0.65 -0.00 +0.007 A
DOCKED: HETATM 2 C2 BEN A 1 -1.633 12.658 15.174 -0.63 -0.02 +0.015 A
DOCKED: HETATM 3 C3 BEN A 1 -1.622 12.868 13.789 +0.72 -0.00 +0.001 A
DOCKED: HETATM 4 C4 BEN A 1 -1.985 14.116 13.259 -0.50 -0.00 +0.000 A
DOCKED: HETATM 5 C5 BEN A 1 -2.354 15.144 14.130 +1.00 -0.00 +0.001 A
DOCKED: HETATM 6 C6 BEN A 1 -2.359 14.909 15.503 -0.58 -0.01 +0.015 A
DOCKED: ENDROOT
DOCKED: BRANCH 1 7
DOCKED: HETATM 7 C BEN A 1 -2.026 13.460 17.389 -0.63 -0.04 +0.102 C
DOCKED: HETATM 8 N2 BEN A 1 -2.122 14.489 18.214 -0.54 +0.08 -0.385 N
DOCKED: HETATM 9 H22 BEN A 1 -2.311 15.409 17.816 -0.01 -0.03 +0.157 HD
DOCKED: HETATM 10 H21 BEN A 1 -2.137 14.333 19.222 -0.03 -0.03 +0.157 HD
DOCKED: BRANCH 7 11
DOCKED: HETATM 11 N1 BEN A 1 -1.782 12.269 17.905 -0.03 +0.17 -0.385 N
DOCKED: HETATM 12 H12 BEN A 1 -0.878 11.838 17.715 -0.42 -0.05 +0.157 HD
DOCKED: HETATM 13 H11 BEN A 1 -2.514 11.731 18.370 -0.45 -0.06 +0.157 HD
DOCKED: ENDBRANCH 7 11
DOCKED: ENDBRANCH 1 7
DOCKED: TORSDOF 2
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
FINAL DOCKED STATE:
________________________
Run: 7 / 40
Time taken for this run: 98.703s
DOCKED: MODEL 7
DOCKED: USER Run = 7
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -5.15 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -5.75 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -5.61 kcal/mol
DOCKED: USER Electrostatic Energy = -0.13 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = +0.19 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +0.60 kcal/mol
DOCKED: USER (4) Unbound System's Energy = +0.19 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK 2 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C1_1 and C_7
DOCKED: REMARK 2 A between atoms: C_7 and N1_8
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: HETATM 1 C1 BEN A 1 -1.930 14.121 16.491 -0.61 -0.00 +0.007 A
DOCKED: HETATM 2 C2 BEN A 1 -1.025 13.641 17.400 -0.61 -0.00 +0.015 A
DOCKED: HETATM 3 C3 BEN A 1 -0.969 14.191 18.687 -0.59 -0.00 +0.001 A
DOCKED: HETATM 4 C4 BEN A 1 -1.842 15.229 19.051 -0.47 -0.00 +0.000 A
DOCKED: HETATM 5 C5 BEN A 1 -2.765 15.702 18.116 -0.42 -0.00 +0.001 A
DOCKED: HETATM 6 C6 BEN A 1 -2.798 15.140 16.843 -0.58 -0.01 +0.015 A
DOCKED: ENDROOT
DOCKED: BRANCH 1 7
DOCKED: HETATM 7 C BEN A 1 -1.978 13.581 15.210 -0.76 -0.09 +0.102 C
DOCKED: HETATM 8 N2 BEN A 1 -2.545 14.261 14.229 -0.70 +0.44 -0.385 N
DOCKED: HETATM 9 H22 BEN A 1 -2.820 15.227 14.409 -0.59 -0.16 +0.157 HD
DOCKED: HETATM 10 H21 BEN A 1 -2.580 13.866 13.290 -0.45 -0.28 +0.157 HD
DOCKED: BRANCH 7 11
DOCKED: HETATM 11 N1 BEN A 1 -1.621 12.330 14.977 -0.63 +0.50 -0.385 N
DOCKED: HETATM 12 H12 BEN A 1 -1.810 11.941 14.054 -0.51 -0.36 +0.157 HD
DOCKED: HETATM 13 H11 BEN A 1 -1.288 11.724 15.726 -0.38 -0.17 +0.157 HD
DOCKED: ENDBRANCH 7 11
DOCKED: ENDBRANCH 1 7
DOCKED: TORSDOF 2
DOCKED: TER
DOCKED: ENDMDL
________________________________________________________________________________
FINAL DOCKED STATE:
________________________
Run: 8 / 40
Time taken for this run: 98.703s
DOCKED: MODEL 8
DOCKED: USER Run = 8
DOCKED: USER
DOCKED: USER Estimated Free Energy of Binding = -1.37 kcal/mol [=(1)+(2)+(3)-(4)]
DOCKED: USER
DOCKED: USER (1) Final Intermolecular Energy = -1.97 kcal/mol
DOCKED: USER vdW + Hbond + desolv Energy = -1.91 kcal/mol
DOCKED: USER Electrostatic Energy = -0.05 kcal/mol
DOCKED: USER (2) Final Total Internal Energy = +0.18 kcal/mol
DOCKED: USER (3) Torsional Free Energy = +0.60 kcal/mol
DOCKED: USER (4) Unbound System's Energy = +0.18 kcal/mol
DOCKED: USER
DOCKED: USER
DOCKED: REMARK 2 active torsions:
DOCKED: REMARK status: ('A' for Active; 'I' for Inactive)
DOCKED: REMARK 1 A between atoms: C1_1 and C_7
DOCKED: REMARK 2 A between atoms: C_7 and N1_8
DOCKED: USER x y z vdW Elec q Type
DOCKED: USER _______ _______ _______ _____ _____ ______ ____
DOCKED: ROOT
DOCKED: HETATM 1 C1 BEN A 1 -1.839 13.845 16.227 -0.63 -0.00 +0.007 A
DOCKED: HETATM 2 C2 BEN A 1 -1.638 12.729 15.459 -0.66 -0.01 +0.015 A
DOCKED: HETATM 3 C3 BEN A 1 -1.720 12.819 14.063 +0.33 -0.00 +0.001 A
DOCKED: HETATM 4 C4 BEN A 1 -2.001 14.049 13.448 -0.54 -0.00 +0.000 A
DOCKED: HETATM 5 C5 BEN A 1 -2.195 15.180 14.245 +1.06 -0.00 +0.001 A
DOCKED: HETATM 6 C6 BEN A 1 -2.111 15.063 15.630 -0.55 -0.01 +0.015 A
DOCKED: ENDROOT
DOCKED: BRANCH 1 7
DOCKED: HETATM 7 C BEN A 1 -1.768 13.752 17.613 -0.66 -0.03 +0.102 C
DOCKED: HETATM 8 N2 BEN A 1 -1.882 12.574 18.202 -0.54 +0.13 -0.385 N
DOCKED: HETATM 9 H22 BEN A 1 -1.889 11.741 17.614 -0.60 -0.12 +0.157 HD
DOCKED: HETATM 10 H21 BEN A 1 -1.830 12.506 19.218 -0.11 -0.03 +0.157 HD
DOCKED: BRANCH 7 11
DOCKED: HETATM 11 N1 BEN A 1 -1.757 14.831 18.375 -0.54 +0.07 -0.385 N
DOCKED: HETATM 12 H12 BEN A 1 -2.648 15.282 18.583 -0.03 -0.02 +0.157 HD