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Classical force-field for peptides containing 4-fluorinated proline residues (or any canonical peptide). Includes a proline ring pucker correction

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ajaymur91/pucker-correction

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Requirements:

Description:

This code creates a classical force-field for a peptide containing 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
  • 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

Usage:

bash main.sh #(guides the user through the process)

main.sh calls several scripts in the following order:

tleap -f tleap_script.txt > tleap.LOG  # create peptide based on tleap script 
bash fix_pro_omega.sh                  # fix omega dihedrals potential barriers for Xaa-Pro peptide bonds (This is optional)  
python convert2_gmx_charmm.py          # Convert from amber to gromacs and charmm types
bash make_pucker_correct_plumed.sh     # creates plumed.dat that adds pucker correction as external bias

The only thing the user has to do is edit tleap_script.txt

For instance, you can do

amber=sequence{ACE GLY GLY PSF PRF NME} #(edit this inside tleap_script.txt)

solvatebox amber TIP3PBOX 10 #(creates 1nm^3 tip3p waterbox. edit this inside tleap_script.txt)

  • Running bash main.sh creates the force-field for the chosen peptide in gromacs_ff/ charmm_ff/ and amber_ff/ folders along with the plumed.dat file that adds the pucker correction as an external bias from pucker_correction_data folder

  • to implement the ring puckering correction as external bias, you will need to patch your MD code (gromacs/ amber/ openMM) with Plumed (https://github.com/plumed/plumed2). The simplest way to do this (for gromacs atleast) is to use spack package manager. https://github.com/spack/spack For example, installing gromacs patched with plumed is as easy as:

spack install gromacs +plumed

Citation:

Article: DOI

Code: DOI

Slides (Talk at APS)

https://absuploads.aps.org/presentation.cfm?pid=18448

or

https://doi.org/10.6084/m9.figshare.12302780

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Classical force-field for peptides containing 4-fluorinated proline residues (or any canonical peptide). Includes a proline ring pucker correction

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