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Developer: Abdelazim M. A. Abdelgawwad.
Institut de Ciència  Molecular (ICMol), Universitat de València, P.O. Box 22085, València 46071, Spain

Distributed under the GNU LESSER GENERAL PUBLIC LICENSE Version 2.1, February 1999
Copyright 2024 Abdelazim M. A. Abdelgawwad, Universitat de València. E-mail: abdelazim.abdelgawwad@uv.es 

**easyPARM** is a computational tool developed by **Abdelazim M. A. Abdelagawwad** under the supervision
of **Dr. Antonio FrancÃ©s-Monerris** at the Institut de CiÃ¨ncia Molecular (ICMol), Universitat de ValÃ¨ncia. 
Its primary purpose is to simplify the derivation of force field parameters for metal-containing molecular 
systems and to enable charge restraints on specific atoms.

## How to cite 
If you use this code in your research, please cite the original article associated with the code.

## Key Features
1. **Force Field Parameter Generation**: easyPARM uses the Seminario method [1] to derive bond-stretching 
and bond-angle bending parameters for metal-containing systems. These parameters are optimized for use 
with the AMBER software suite [2], based on the Hessian matrix from frequency calculations performed with 
Gaussian 09 or 16. Additionally, the tool can generate parameters for non-metal systems using GAFF or the 
AMBER force fields. 

2. **Charge Restraint Using REsP Fitting**: easyPARM also supports charge restraints using the Restrained 
Electrostatic Potential (REsP) fitting approach [3]. This ensures that the electrostatic potential around 
the molecule is accurate and physically meaningful.

## Prerequisites
Before running easyPARM, you will need the following input files:

1. **Formatted Checkpoint File (.fchk)**: Contains the hessian matrix and data from a previous quantum 
chemistry calculation (Gaussian) [4].
2. **Optimized Structure (XYZ Format)**: A file with the optimized molecular geometry in XYZ format.
3. **Gaussian Charge Output**: Charge distribution information (ESP charge) generated from a Gaussian 
calculation.

## Running easyPARM
**Method 1: Direct Script Execution**
To run the script directly, use the following command:

`./easyPARM.sh`

**Method 2: Using an Alias**
For easier access, you can create an alias in your .bashrc file:

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

## Installation Requirements

**Python 3**: Ensure Python 3 is installed in your environment.

**Required Python Packages**: The script depends on scipy and periodictable. Install them using pip if not 
already available:

`pip install scipy` 

`pip install periodictable`

Additional package requirements may arise during execution. If prompted, install them via pip or contact 
us for assistance: abdelazim.abdelgawwad@uv.es.

## Important Notes
- Ensure that input files are correctly formatted and placed in the appropriate directory before running 
the script.
- The script processes these inputs to generate the necessary AMBER force field parameters, which will be 
output in the same directory.
- Output files will include `.mol2`, `.lib`, `.pdb`, and `.frcmod` files for use in molecular dynamics 
simulations.

## Molecular Dynamics Considerations
When using the mol2 and frcmod files to generate a library, tleap in AMBER may not correctly assign 
connectivity and atomic numbers for metals. To avoid this issue, we recommend using the pre-generated 
`.lib` and `.frcmod files`, which contain all necessary data.

Your leap script should include:


`loadamberparams COMPLEX.frcmod`

`loadoff COMPLEX.lib`

## Contact & Support
For troubleshooting or additional assistance, please refer to the documentation in our GitHub repository. 
You can also reach us via email at: abdelazim.abdelgawwad@uv.es.

## How to cite 
If you use this code in your research, please cite the original article associated with the code.

### References
[1]	Seminar, J. M. Calculation of Intramolecular Force Fields from Second-Derivative Tensors; 1996.

[2]	Case, D. A.; Aktulga, H. M.; Belfon, K.; Ben-Shalom, I. Y.; Brozell, S. R.; Cerutti, D. S.; Cheatham 
III, T. E.; Cisneros, G. A.; Cruzeiro, V. W. D.; Darden, T. A.; Duke, R. E.; Giambasu, G.; Gilson, M. K.; 
Gohlke, H.; Goetz, A. W.; Harris, R.; Izadi, S.; Izmailov, S. A.; Jin, C.; Kasavajhala, K.; Kaymak, M. C.; King, 
E.; Kovalenko, A.; Kurtzman, T.; Lee, T. S.; LeGrand, S.; Li, P.; Lin, C.; Liu, J.; Luchko, T.; Luo, R.; 
Machado, M.; Man, V.; Manathunga, M.; Merz, K. M.; Miao, Y.; Mikhailovskii, O.; Monard, G.; Nguyen, H.; 
Oâ€™Hearn, K. A.; Onufriev, A.; Pan, F.; Pantano, S.; Qi, R.; Rahnamoun, A.; D.R. Roe; Roitberg, A.; Sagui, C.; 
Schott-Verdugo, S.; Shen, J.; Simmerling, C. L.; Skrynnikov, N. R.; Smith, J.; Swails, J.; Walker, R. C.; Wang, 
J.; Wei, H.; Wolf, R. M.; Wu, X.; Xue, Y.; York, D. M.; Zhao, S.; Kollman, P. A. Amber 20. Amber 20 2021, San 
Francisco.      https://ambermd.org/

[3]	Comell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. Application of RESP Charges to calculate 
conformational energies, hydrogen bond energies, and free energies of solvation. Journal of American Chemical 
Society 1993, 115 (7), 9620â€“9631.   https://doi.org/10.1021/ja00074a030

[4] Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. a.; Cheeseman, J. R.; Scalmani, 
G.; Barone, V.; Petersson, G. a.; Nakatsuji, H.; Li, X.; Caricato, M.; Marenich, a. V.; Bloino, J.; Janesko, 
B. G.; Gomperts, R.; Mennucci, B.; Hratchian, H. P.; Ortiz, J. V.; Izmaylov, a. F.; Sonnenberg, J. L.; 
Williams; Ding, F.; Lipparini, F.; Egidi, F.; Goings, J.; Peng, B.; Petrone, A.; Henderson, T.; Ranasinghe, 
D.; Zakrzewski, V. G.; Gao, J.; Rega, N.; Zheng, G.; Liang, W.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; 
Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Throssell, K.; Montgomery 
Jr., J. a.; Peralta, J. E.; Ogliaro, F.; Bearpark, M. J.; Heyd, J. J.; Brothers, E. N.; Kudin, K. N.; 
Staroverov, V. N.; Keith, T. a.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, a. P.; Burant, J. C.; 
Iyengar, S. S.; Tomasi, J.; Cossi, M.; Millam, J. M.; Klene, M.; Adamo, C.; Cammi, R.; Ochterski, J. W.; 
Martin, R. L.; Morokuma, K.; Farkas, O.; Foresman, J. B.; Fox, D. J. G16_C01. 2016, p Gaussian 16, Revision C.01, 
Gaussian, Inc., Wallinford, CT, USA.       https://gaussian.com/ 

