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
CHARGE_METHOD = 1

# 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 = 2                    # 1 = AMBER, 2 = GAFF, 3 = GAFF2
CHARGE_OUTPUT = CHARGES.log    # Charge output file (.log, .out, .vpot, or .dat)

# Quantum Mechanics Output Format
# 1 = Orca Output, 2 = Gaussian Output, 3 = Gaussian Checkpoint, 
# 4 = Gaussian Formatted Checkpoint, 5 = Gamess 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 = complex2.fchk        # For QM_OUTPUT = 4
# GAMESS_OUTPUT = output.dat     # For QM_OUTPUT = 5

# Metalloprotein Configuration
METALLOPROTEIN = no              # Is this a metalloprotein? (yes/no)
# PDB_FILE = protein.pdb         # PDB file (only if METALLOPROTEIN = yes)

RESID_ID = no                    # 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 modify the appropriate lines according to your system requirements. Once you have prepared 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 any variable is missing in your input file, check the message that appears 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 there is a problem with your input configuration, the code will automatically enter interactive mode
If you don’t provide an input file, the code will default to interactive mode
Make sure to uncomment only the parameters relevant to your chosen configuration

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