diff --git a/abfe/abfe_alchemy_md.py b/abfe/abfe_alchemy_md.py index b47676b..5678e48 100644 --- a/abfe/abfe_alchemy_md.py +++ b/abfe/abfe_alchemy_md.py @@ -145,7 +145,7 @@ def _parse_args(): ) boresch_grp.add_argument( '-dc', '--dihedral_const', default=100.0, type=float, - help='Force constant for dihedral restraint, in kcal/mol' + help='Force constant for dihedral restraint, in kcal/mol/radian^2' ) boresch_grp.add_argument( '-rs', '--restraint_seed', type=int, default=None, @@ -843,4 +843,4 @@ def _add_boresch_restraint(args, prmtop, lig_masks, rec_masks, lig_idx, rst_refs _, out, _ = ctools.command_caller(command=shcmd, shell=True) jobid = re.findall(r"job (.*?)\n", str(out)) with open('slurm_jobid.log', 'w') as f: - f.writelines(f'INFO: ARRAY JOB ID {jobid[0]}') \ No newline at end of file + f.writelines(f'INFO: ARRAY JOB ID {jobid[0]}') diff --git a/testing/abfe_testing/config.yaml b/testing/abfe_testing/config.yaml index 4828e0e..7224e73 100644 --- a/testing/abfe_testing/config.yaml +++ b/testing/abfe_testing/config.yaml @@ -74,7 +74,7 @@ }, "bond_const": 10.0, # force constant for Boresch-style bond restraint, in kcal/mol/A^2 "angle_const": 100.0, # force constant for Boresch-style angle restraint, in kcal/mol/radian^2 - "dihedral_const": 100.0, # force constant for Boresch-style dihedral restraint, in kcal/mol + "dihedral_const": 100.0, # force constant for Boresch-style dihedral restraint, in kcal/mol/radian^2 "abfe_solvated_vdw_lambdas": [ # lambda windows for solvated decoupled leg 0.0, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45, diff --git a/testing/ahfe_testing/config.yaml b/testing/ahfe_testing/config.yaml index c6912f3..63777da 100644 --- a/testing/ahfe_testing/config.yaml +++ b/testing/ahfe_testing/config.yaml @@ -74,7 +74,7 @@ }, "bond_const": 10.0, # force constant for Boresch-style bond restraint, in kcal/mol/A^2 "angle_const": 100.0, # force constant for Boresch-style angle restraint, in kcal/mol/radian^2 - "dihedral_const": 100.0, # force constant for Boresch-style dihedral restraint, in kcal/mol + "dihedral_const": 100.0, # force constant for Boresch-style dihedral restraint, in kcal/mol/radian^2 "abfe_solvated_vdw_lambdas": [ # lambda windows for solvated decoupled leg 0.0, 0.05, 0.10, 0.15, 0.20, 0.25, 0.30, 0.35, 0.40, 0.45,