Input Generator

Input Filename:
Enter the desired file name for the SparcleQC input file that will be created
PDB File: Enter the path to the complex PDB (amber) or protein PDB (charmm)
The path should be either absolute or relative to where the input file will be executed
E.x., "example.pdb", "user/documents/example.pdb"
Cutoff Radius (Å): Enter the cutoff radius (float) that determines which atoms are included in the QM region
Seed: Choose if the QM region should be defined by distance to any atom in the ligand or to a specific atom
If choosing a specific atom, specify the file that contains that atom with the corresponding atom serial number (atomid)

Ligand: Seed ID: Seed File:

Charge Scheme: Z1 Z2 Z3 DZ1 DZ2 DZ3 BRC BRC2 BRCD Choose a charge scheme that determines how boundary MM charges are redistributed
Specifics on each charge scheme can be found in the user guide
Forcefield: If CHARMM is selected, charges must be precomputed using CHARMM-GUI
If Amber is selected, SparcleQC will obtain point charges automatically

CHARMM

Enter the path to the CHARMM parameter files
The path should be either absolute or relative to where the input file will be executed

Topology Path:

Parameter Path:

Amber

Enter the desired Amber forcefield (e.g. ff19SB)
If other forcefields are needed to obtain point charges for the system enter them here
If the checkbox below is checked, SparcleQC will cap the terminal residues with ACE and NME

Forcefield:

Other Forcefields (Optional):

Cap Terminal Residues?

Water Charges: Enter the desired water model (e.g. OPC)
If you wish to override these charges, check the box below and you will be able to manually add charges for either a 3 or 4 point water

Water Model:

Add Your Own Water Charges (Optional)

3-point Water Model

4-point Water Model

Oxygen Charge:

Hydrogen Charge:

Extra Point Charge:

Software: Choose the desired quantum chemistry software
After choosing, optional software specific options will be available

NWChem

NWChem Settings (Optional):
Scratch Directory:
Permanent Directory:
SCF Options Dictionary:
DFT Options Dictionary:
Memory:

Q-Chem

Q-Chem Settings (Optional):
Additional Options Dictionary:
SAPT Options (Dictionary):

Psi4

Psi4 Settings (Optional):
FISAPT Partition
Do FSAPT
Additional Options Dictionary:
Num Threads:
Memory:

Ligand Charge: Enter the charge of the ligand
Level of Theory: Enter desired method (e.g. hf) and basis set (e.g. cc-pvdz) for the QM computation

Method: Basis Set:

Other Features: Additional optional features are outlined in the user guide

Template Path (Optional):

Counterpoise Correct?

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