Non-Interactive Mode

Installation

1. Downloading easyPARM

Ensure you have the latest version that supports non-interactive mode by cloning the repository from GitHub:

git clone https://github.com/Abdelazim-Abdelgawwad/easyPARM.git

2. Non-Interactive Mode Overview

Thanks to Floris Löffler for suggesting the implementation of a non-interactive mode, which is particularly useful when processing multiple structures to save time. The code can now run in either non-interactive or interactive mode depending on how it’s submitted.

Using Non-Interactive Mode

To use non-interactive mode, create an input configuration file with your system parameters and submit the code as shown below.

Sample Input Configuration File

# easyPARM Input Configuration File
# Modify this template for your specific needs

# Basic Configuration
PARAMETERIZE = 1                 # Generate molecular parameters (1 = yes)
AMBER_CONFIG = 1                 # AMBER configuration (1 = loaded AMBER, 2 = AMBER path)
# AMBER_PATH = /path/to/AMBER    # For AMBER_CONFIG = 2 
CHARGE = 0                       # Total charge of the molecule
MULTIPLICITY = 1                 # Spin multiplicity of the molecule
STRUCTURE_FILE = OPTIMIZED.xyz   # Optimized molecular structure file name

# Charge Calculation Method
# 1 = RESP (GAUSSIAN), 2 = CHELPG (ORCA), 3 = RESP (ORCA), 
# 4 = RESP (GAMESS), 5 = GAMESS CHARGES, 6= PSI4 (RESP)
CHARGE_METHOD = 1

# PSI4 controls whether to run a new calculation:
#   ON  -> run calculation (not done yet)
#   OFF -> skip calculation (already done)
# PSI4 = ON

# Parameters for charge calculation
# These parameters depend on your CHARGE_METHOD selection

# RESP (GAUSSIAN) specific parameters (only needed if CHARGE_METHOD = 1)
INPUT_FORMAT = 1                 # 1 = .log file, 2 = .gesp file
METHOD = 1                       # 1 = RESP, 2 = Mulliken, 3 = ESP, 4 = AM1-BCC

# Required for all charge methods
ATOM_TYPE = 3                    # 1 = AMBER, 2 = GAFF, 3 = GAFF2
CHARGE_OUTPUT = mol2_comp.log    # Charge output file (.log, .out, .vpot, or .dat)

# Quantum Mechanics Frequency Output Format
# 1 = Orca Output, 2 = Gaussian Output, 3 = Gaussian Checkpoint, 
# 4 = Gaussian Formatted Checkpoint, 5 = Gamess Output, 6= PSI4 Output
QM_OUTPUT = 4

# QM output files based on QM_OUTPUT selection
# Uncomment the appropriate options for your QM_OUTPUT value

# GAUSSIAN_OUTPUT = output.log   # For QM_OUTPUT = 2
# ORCA_OUTPUT = output.out       # For QM_OUTPUT = 1
# ORCA_HESS = output.hess        # For QM_OUTPUT = 1
# CHK_FILE = output.chk          # For QM_OUTPUT = 3
# GAUSSIAN_CONFIG = 1            # For QM_OUTPUT = 3 (1 = loaded gaussian, 2 = GAUSSIAN PATH)
# GAUSSIAN_PATH = /path/to/g16   # For GAUSSIAN_CONFIG = 2
FCHK_FILE = complex1.fchk        # For QM_OUTPUT = 4
# GAMESS_OUTPUT = output.dat     # For QM_OUTPUT = 5
# PSI4 SETTINGS For QM_OUTPUT = 6
# CPU = 6                        # Number of CPU cores to use
# MEMORY = 10GB                  # Amount of memory to use formats: 5GB, 500MB, 1000MB
# METHOD = B3LYP                 # Functional defaults to B3LYP
# BASIS_SET = 6-31G*, DEF2-SVP   # Basis set specification (optional) defaults are: 6-31G* (non-metals), LANL2DZ (metals)


# Metalloprotein & Metalnucleic Configuration
METALLOPROTEIN = no              # Is this a metalloprotein? (yes/no)
METALLONUCLEIC = no              # Is this a metal bound nucleic acid (yes/no)

# PDB_FILE = amber.pdb           # PDB file (only if METALLOPROTEIN OR METALLONUCLEIC = yes)

# The selection of the force field to describe the metal-coordinated standard residues. 
# In case of METALLOPROTEIN. 1 = AMBER-fb15, 2 = ff12SB, 3= ff14SB, 4 =  ff19SB
# In case of METALLONUCLEIC. 1 = DNA-BSC0, 2 = DNA-BSC1, 3 = DNA-OL15, 4 = DNA-OL21, 5 = DNA-OL24, 6 = RNA-OL3
# FF_TYPE = 2                  

RESID_ID = yes                   # Define residue ID? (yes/no)
RESID_NAME = LIG                 # Three-letter residue name (only if RESID_ID = yes)

# Force Field Configuration
CHARMM_FF = no                   # Generate CHARMM force field? (yes/no)

# Charge Restraints
CHARGE_RESTRAIN = no             # Apply charge restraints? (yes/no)
# NUM_ATOMS = 1                  # Number of atoms with charge restraints (only if CHARGE_RESTRAIN = yes)
# ATOM1 = 1 -0.834               # Atom number and charge value for restraint 1
# ATOM2 = 2 0.417                # Atom number and charge value for restraint 2
# CHARGE_FILE = output.vpot      # Charge file (.vpot, .log, .out, .dat)

Uncomment and adjust the relevant lines according to your system requirements. After preparing your input file, you can run the code using one of the methods described below.

Running the Script

Method 1: Direct Execution

To run easyPARM.sh directly:

Navigate to your working directory
Execute the script from the easyPARM directory:

../easyPARM.sh INPUT_NAME

⚠️ Important: If your input file lacks any required variable, review the message printed at the beginning of the execution.

Method 2: Using an Alias (Recommended)

To run easyPARM from any location in your terminal:

Create an alias by adding the following line to your ~/.bashrc or ~/.bash_profile file:

alias easyPARM='/full/path/to/easyPARM.sh'

Apply the changes:

source ~/.bashrc   # or source ~/.bash_profile

Now you can simply run:

easyPARM INPUT_NAME

Important Notes

If your input configuration contains an error, the code will automatically switch to interactive mode.
If no input file is provided, the code will also default to interactive mode.
Make sure to uncomment only the parameters relevant to your selected configuration.

For additional support, please consult the GitHub Issues Page or contact the development team.