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use user defined amber masks #454
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@marioernestovaldes
marioernestovaldes committed Jan 18, 2024
1 parent 70c18e3 commit 8a49645
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Showing 4 changed files with 115 additions and 112 deletions.
15 changes: 9 additions & 6 deletions GMXMMPBSA/createinput.py
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Original file line number Diff line number Diff line change
Expand Up @@ -197,19 +197,22 @@ def create_inputs(INPUT, prmtop_system, pre):
com_input = deepcopy(INPUT)
rec_input = deepcopy(INPUT)
lig_input = deepcopy(INPUT)
(com_input['gb']['qmmask'], rec_input['gb']['qmmask'],
lig_input['gb']['qmmask']) = prmtop_system.Mask(INPUT['gb']['qm_residues'], in_complex=False)

if INPUT['gb']['exclude_backbone']:
com_input['gb']['qmmask'] = f"({com_input['gb']['qmmask']} & !@N,H,CA,HA,C,O)"
rec_input['gb']['qmmask'] = f"({rec_input['gb']['qmmask']} & !@N,H,CA,HA,C,O)"
lig_input['gb']['qmmask'] = f"({lig_input['gb']['qmmask']} & !@N,H,CA,HA,C,O)"
if INPUT['gb']['com_qmmask'] or INPUT['gb']['rec_qmmask'] or INPUT['gb']['lig_qmmask']:
(com_input['gb']['qmmask'], rec_input['gb']['qmmask'],
lig_input['gb']['qmmask']) = (INPUT['gb']['com_qmmask'], INPUT['gb']['rec_qmmask'],
INPUT['gb']['lig_qmmask'])
logging.warning(f'Ignoring residues from qm_residues variable. Using user defined masks instead...')
else:
(com_input['gb']['qmmask'], rec_input['gb']['qmmask'],
lig_input['gb']['qmmask']) = prmtop_system.Mask(INPUT['gb']['qm_residues'], in_complex=False)

if not com_input['gb']['qmmask']:
raise AmberError('No valid QM residues chosen!')
com_input['gb']['qm_theory'] = "'%s'" % com_input['gb']['qm_theory']
com_input['gb']['qmmask'] = "'%s'" % com_input['gb']['qmmask']
com_input['gb']['qmcharge'] = com_input['gb']['qmcharge_com']

# check if alpb
if com_arad:
com_input['gb']['arad'] = com_arad
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29 changes: 16 additions & 13 deletions GMXMMPBSA/input_parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -401,26 +401,26 @@ def Parse(self, filename):

input_file.addNamelist('general', 'general',
[
# Basic options
# Basic options
['sys_name', str, '', 'System name'],
['startframe', int, 1, 'First frame to analyze'],
['endframe', int, 9999999, 'Last frame to analyze'],
['interval', int, 1, 'Number of frames between adjacent frames analyzed'],

# Parameters options
# Parameters options
['forcefields', list, 'oldff/leaprc.ff99SB, leaprc.gaff', 'Define the force field to build '
'the Amber topology'],
['ions_parameters', int, 1, 'Define ions parameters to build the Amber topology'],
['PBRadii', int, 3, 'Define PBRadii to build amber topology from GROMACS files'],
['temperature', float, 298.15, 'Temperature'],

# Entropy options
# Entropy options
['qh_entropy', int, 0, 'Do quasi-harmonic calculation'],
['interaction_entropy', int, 0, 'Do Interaction Entropy calculation'],
['ie_segment', int, 25, 'Trajectory segment to calculate interaction entropy'],
['c2_entropy', int, 0, 'Do C2 Entropy calculation'],

# Miscellaneous options
# Miscellaneous options
['assign_chainID', int, 0, 'Assign chains ID'],
['exp_ki', list, [0.0], 'Experimental Ki in nM', float],
['full_traj', int, 0, 'Print a full traj. AND the thread trajectories'],
Expand Down Expand Up @@ -450,12 +450,15 @@ def Parse(self, filename):
['qm_theory', str, '', 'Semi-empirical QM theory to use'],
['qm_residues', str, '', 'Residues to treat with QM'],

['exclude_backbone', int, 0, 'Exclude backbone atoms from residues to treat with QM'],
['com_qmmask', str, '', 'Mask specifying the quantum atoms in complex'],
['rec_qmmask', str, '', 'Mask specifying the quantum atoms in receptor'],
['lig_qmmask', str, '', 'Mask specifying the quantum atoms in ligand'],

# TODO: deprecated since 1.5.0. Automatic charge assignment
# deprecated since 1.5.0. Automatic charge assignment except when using user defined masks
['qmcharge_com', int, 0, 'Charge of QM region in complex'],
['qmcharge_lig', int, 0, 'Charge of QM region in ligand'],
['qmcharge_rec', int, 0, 'Charge of QM region in receptor'],

['qmcut', float, 9999, 'Cutoff in the QM region'],
['scfconv', float, 1.0e-8, 'Convergence criteria for the SCF calculation, in kcal/mol'],
['peptide_corr', int, 0, 'Apply MM correction to peptide linkages'],
Expand All @@ -474,7 +477,7 @@ def Parse(self, filename):
['alpb', int, 1, 'Specifies if ALBP correction is to be used.'],
['epsin', float, 1.0, 'Sets the dielectric constant of the solute region'],
['epsout', float, 78.5, 'Sets the implicit solvent dielectric constant for the solvent'],
# FIXME: convert to M
# FIXME: convert to M
['istrng', float, 0.0, 'Sets the ionic strength in M for the GB equation'],
['rs', float, 0.52, 'Dielectric boundary shift compared to the '
'molecular surface (only relevant for the -chagb option)'],
Expand All @@ -494,7 +497,7 @@ def Parse(self, filename):

input_file.addNamelist('pb', 'pb',
[
# Basic input options
# Basic input options
['ipb', int, 2, 'Dielectric model for PB'],
['inp', int, 1, 'Nonpolar solvation method'],
['sander_apbs', int, 0, 'Use sander.APBS?'],
Expand Down Expand Up @@ -537,7 +540,7 @@ def Parse(self, filename):
'electrostatic focussing calculation'],
['npbgrid', int, 1, 'Sets how often the finite-difference grid is regenerated'],

# Options to compute energy and forces
# Options to compute energy and forces
['bcopt', int, 5, 'Boundary condition option'],
['eneopt', int, 2, 'Compute electrostatic energy and forces'],
['frcopt', int, 0, 'Output for computing electrostatic forces'],
Expand All @@ -546,7 +549,7 @@ def Parse(self, filename):
['cutnb', float, 0.0, 'Cutoff for nonbonded interations'],
['nsnba', int, 1, 'Sets how often atom-based pairlist is generated'],

# Options to select a non-polar solvation treatment
# Options to select a non-polar solvation treatment
['decompopt', int, 2, 'Option to select different decomposition schemes when INP = 2'],
['use_rmin', int, 1, 'The option to set up van der Waals radii'],
['sprob', float, 0.557, 'Solvent probe radius for SASA used to compute the dispersion term'],
Expand Down Expand Up @@ -646,15 +649,15 @@ def Parse(self, filename):

input_file.addNamelist('nmode', 'nmode',
[
# Basic Options
# Basic Options
['nmstartframe', int, 1, 'First frame to analyze for normal modes'],
['nmendframe', int, 1000000, 'Last frame to analyze for normal modes'],
['nminterval', int, 1, 'Interval to take snapshots for normal mode analysis'],
# Parameters options
# Parameters options
['nmode_igb', int, 1, 'GB model to use for normal mode calculation'],
['nmode_istrng', float, 0, 'Ionic strength for GB model (M)'],
['dielc', float, 1, 'Dielectric constant'],
# Minimization options
# Minimization options
['drms', float, 0.001, 'Minimization gradient cutoff'],
['maxcyc', int, 10000, 'Maximum number of minimization cycles'],
], trigger='nmoderun')
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