# Provide informative titles MOLECULE1-TITLE = Dimethylphosphate MOLECULE2-TITLE = Deoxyadenosine # Providing the total charge for molecule 1 is mandatory MOLECULE1-TOTCHARGE = -1 # Providing the total charge for molecule 2 is not mandatory MOLECULE2-TOTCHARGE = 0 # Define two inter-mcc1 between molecule 1 & molecule 2 # Atom C2 (index 10; involved in the constraint) is connected to O5' (index 9; not involved in the constraint) in molecule 1; # Atom 1 (involved in the constraint) of molecule 2 bears also the O5' atom name MOLECULE-INTER-MCC1 = 0.0 | 1 2 | 10 11 12 13 | 1 2 # Atom C1 (index 1; involved in the constraint) is connected to O3' (index 5; not involved in the constraint) in molecule 1; # Atom 3 (involved in the constraint) of molecule 2 bears also the O3' atom name MOLECULE-INTER-MCC1 = 0.0 | 1 2 | 1 2 3 4 | 3 4 # Thus, the two following constraints would be inappropriate: # MOLECULE-INTER-MCC1 = 0.0 | 1 2 | 10 11 12 13 | 3 4 # MOLECULE-INTER-MCC1 = 0.0 | 1 2 | 1 2 3 4 | 1 2 # Adding additional charge constraints to get compatibility between the Amber and PyRED force field libraries: # tleap -f leaprc.ff99SB -> old FF taken as an example # > charge DA.1 # Total unperturbed charge: -1.000000 # Total perturbed charge: -1.000000 # > charge DA3.1 # Total unperturbed charge: -0.692100 # Total perturbed charge: -0.692100 # > charge DA5.1 # Total unperturbed charge: -0.307900 # Total perturbed charge: -0.307900 # > charge DA.1.O3' # Total unperturbed charge: -0.523200 # Total perturbed charge: -0.523200 # > charge DA.1.P # Total unperturbed charge: 1.165900 # Total perturbed charge: 1.165900 # > charge DA.1.O1P # Total unperturbed charge: -0.776100 # Total perturbed charge: -0.776100 # > charge DA.1.O2P # Total unperturbed charge: -0.776100 # Total perturbed charge: -0.776100 # > charge DA.1.O5' # Total unperturbed charge: -0.495400 # Total perturbed charge: -0.495400 MOLECULE1-INTRA-MCC1 = -0.5232 | 5 | Keep MOLECULE1-INTRA-MCC1 = 1.1659 | 6 | Keep MOLECULE1-INTRA-MCC1 = -0.7761 | 7 | Keep MOLECULE1-INTRA-MCC1 = -0.7761 | 8 | Keep MOLECULE1-INTRA-MCC1 = -0.4954 | 9 | Keep # > charge DAN.1.O5' # Total unperturbed charge: -0.631800 # Total perturbed charge: -0.631800 # > charge DAN.1.H5T # Total unperturbed charge: 0.442200 # Total perturbed charge: 0.442200 # > charge DAN.1.O3' # Total unperturbed charge: -0.654900 # Total perturbed charge: -0.654900 # > charge DAN.1.H3T # Total unperturbed charge: 0.439600 # Total perturbed charge: 0.439600 MOLECULE2-INTRA-MCC1 = -0.6318 | 1 | Keep MOLECULE2-INTRA-MCC1 = 0.4422 | 2 | Keep MOLECULE2-INTRA-MCC1 = -0.6549 | 3 | Keep MOLECULE2-INTRA-MCC1 = 0.4396 | 4 | Keep