diff --git a/abfe/const.py b/abfe/const.py index 449afb4..212682a 100644 --- a/abfe/const.py +++ b/abfe/const.py @@ -24,10 +24,12 @@ PRO_DEFS = { 'ff14SB': {'source': 'leaprc.protein.ff14SB'}, + 'ff19SB': {'source': 'leaprc.protein.ff19SB'}, } PHOSAA_DEFS = { 'phosaa14SB': {'source': 'leaprc.phosaa14SB'}, + 'phosaa19SB': {'source': 'leaprc.phosaa19SB'}, } LIPID_DEFS = { diff --git a/testing/abfe_testing/config.yaml b/testing/abfe_testing/config.yaml index 7224e73..e74a1db 100644 --- a/testing/abfe_testing/config.yaml +++ b/testing/abfe_testing/config.yaml @@ -29,7 +29,7 @@ }, "topology": { "protein_name": "181L", # user-defined protein name - "protein_ff": "ff14SB", # {"ff14SB"} + "protein_ff": "ff14SB", # {"ff14SB", "ff19SB"} "ligand_ff": "gaff2", # {"gaff2"} "cofactor_names": [], # list of strings, e.g. ["CFA", "CFB"] "cofactor_ff": "gaff2", # {"gaff2"} @@ -40,24 +40,24 @@ "com_box_buffer": 8.0, # box buffer for complex, in Angstrom "neutralize": True, # keep system neutral "ionconc": 0.15, # salt concentration, in Molar - "hmr": True, # False: Turn off HMR; True: turn on HMR; for alchemy_md stage + "hmr": False, # False: Turn off HMR; True: turn on HMR; for alchemy_md stage "hmass": 3.024, # hydrogen mass, in amu }, "equilibration": { "dry_run": False, # False: submit; True: only slurm bash script - "timestep": 0.004, # in ps; 0.004 ps if HMR + "timestep": 0.002, # in ps; 0.004 ps if HMR "solvated_length": 5., # simulation time for ligand in water, in ns "complex_length": 5., # simulation time for ligand in binding pocket, in ns "restraintmask": "!:WAT,Cl-,K+,Na+ & !@H=", # specify solute heavy atoms for positional restraint during min-heat-press simulations, in Amber-Mask style "restraint_wt": 10., # set force constant of positional restraint, in kcal/mol/A^2 }, "alchemy_morph": { - "hmr": True, # False: Turn off HMR; True: turn on HMR; for alchemy_md stage + "hmr": False, # False: Turn off HMR; True: turn on HMR; for alchemy_md stage "hmass": 3.024, # hydrogen mass, in amu }, "alchemy_md": { "dry_run": False, # False: submit; True: only slurm bash script - "timestep": 0.004, # in ps; 0.004 ps if HMR + "timestep": 0.002, # in ps; 0.004 ps if HMR "remd": False, # True: turn on; False: turn off, replica-exchange method for FEP production simulation "remd_numexchg": 1000, # 1000 attempts for remd "solvated_length": 5.0, # FEP production simulation time for solvated leg, in ns diff --git a/testing/abfe_testing/dG_components_results.csv b/testing/abfe_testing/dG_components_results.csv deleted file mode 100644 index b7d6546..0000000 --- a/testing/abfe_testing/dG_components_results.csv +++ /dev/null @@ -1,3 +0,0 @@ -,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc,MBAR_dG_complex_vdw,MBAR_dG_complex_cc,MBAR_dG_complex_restraint,MBAR_dG_analytic,TI_dG_complex_vdw,TI_dG_complex_cc,TI_dG_complex_restraint,TI_dG_analytic -phn,5.18,0.00,5.12,0.00,9.66,0.00,-6.06,11.63,9.74,0.00,-6.27,11.63 -bnz,1.06,0.00,1.04,0.00,7.92,0.00,-6.11,11.64,7.75,0.00,-6.71,11.64 diff --git a/testing/abfe_testing/dG_results.csv b/testing/abfe_testing/dG_results.csv deleted file mode 100644 index 96218be..0000000 --- a/testing/abfe_testing/dG_results.csv +++ /dev/null @@ -1,3 +0,0 @@ -,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -phn,1.08,0.10,0.74,0.10 -bnz,-1.33,0.08,-1.78,0.10 diff --git a/testing/ahfe_testing/config.yaml b/testing/ahfe_testing/config.yaml index 63777da..c297e28 100644 --- a/testing/ahfe_testing/config.yaml +++ b/testing/ahfe_testing/config.yaml @@ -40,24 +40,24 @@ "com_box_buffer": 8.0, # box buffer for complex, in Angstrom "neutralize": True, # keep system neutral "ionconc": 0.15, # salt concentration, in Molar - "hmr": True, # False: Turn off HMR; True: turn on HMR; for equilibration stage + "hmr": False, # False: Turn off HMR; True: turn on HMR; for equilibration stage "hmass": 3.024, # hydrogen mass, in amu }, "equilibration": { "dry_run": True, # False: submit; True: only slurm bash script - "timestep": 0.004, # in ps; 0.004 ps if HMR + "timestep": 0.002, # in ps; 0.004 ps if HMR "solvated_length": 5., # simulation time for ligand in water, in ns "complex_length": 5., # simulation time for ligand in binding pocket, in ns "restraintmask": "!:WAT,Cl-,K+,Na+ & !@H=", # specify solute heavy atoms for positional restraint during min-heat-press simulations, in Amber-Mask style "restraint_wt": 10., # set force constant of positional restraint, in kcal/mol/A^2 }, "alchemy_morph": { - "hmr": True, # False: Turn off HMR; True: turn on HMR; for equilibration stage + "hmr": False, # False: Turn off HMR; True: turn on HMR; for equilibration stage "hmass": 3.024, # hydrogen mass, in amu }, "alchemy_md": { "dry_run": True, # False: submit; True: only slurm bash script - "timestep": 0.004, # in ps; 0.004 ps if HMR + "timestep": 0.002, # in ps; 0.004 ps if HMR "remd": False, # True: turn on; False: turn off, replica-exchange method for FEP production simulation "remd_numexchg": 1000, # 1000 attempts for remd "solvated_length": 5.0, # FEP production simulation time for solvated leg, in ns diff --git a/testing/ahfe_testing/dG_components_results.csv b/testing/ahfe_testing/dG_components_results.csv deleted file mode 100644 index ccefb04..0000000 --- a/testing/ahfe_testing/dG_components_results.csv +++ /dev/null @@ -1,4 +0,0 @@ -,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc -phn,5.08,0.00,4.99,0.00 -,MBAR_dG_solvated_vdw,MBAR_dG_solvated_cc,TI_dG_solvated_vdw,TI_dG_solvated_cc -bnz,1.09,0.00,1.03,0.00 diff --git a/testing/ahfe_testing/dG_results.csv b/testing/ahfe_testing/dG_results.csv deleted file mode 100644 index 32fd52b..0000000 --- a/testing/ahfe_testing/dG_results.csv +++ /dev/null @@ -1,4 +0,0 @@ -,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -phn,-5.08,0.06,-4.99,0.07 -,MBAR_dG,MBAR_dG_std,TI_dG,TI_dG_std -bnz,-1.09,0.05,-1.03,0.06