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ajaymur91 authored Jun 26, 2020
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# Description:

This code creates a classical force-field for a peptide containing
4-Fluorinated Proline (non-natural) residues. (ACE-PRF-NME by default, can be changed in tleap_script.txt)
4-Fluorinated Proline residues. (chooses ACE-PRF-NME by default, but can be changed in tleap_script.txt)
Code supports the following 4-fluorinated prolines:
* PRF is 4R-fluoro proline residue
* PSF is 4S-fluoro proline residue

As an example you may choose the following sequence (shown in snapshot below):
ACE-GLY-GLY-PRF-GLY-GLY-NME

* You can use the code for canonical peptides too.
* Creates input files for gromacs or amber or charmm (or openMM).
* Adds a TIP3P waterbox. (1nm^3 default, can be changed in tleap_script.txt)
* All canonical amino acid residues are available too.
* Code also adds a TIP3P waterbox. (1nm^3 default, can be changed in tleap_script.txt)
* Creates force-field parameters and starting configurations for gromacs, amber and charmm (or openMM).
* Creates a plumed.dat file that adds pucker correction for fluorinated proline residues.

You can select a peptide of your choice by editing the tleap_script.txt file.
* As an example you may choose the following sequence (shown in snapshot below):
ACE-GLY-GLY-PRF-GLY-GLY-NME



![Alt text](code.png/code.png.001.png?raw=true "Title")

# Usage:
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