sscake / hps2gmx_topol_converter

This program aims to generate the topology file in GROMACS format to use GROMACS built-in analysis program after the implementation of HydroPathy Scale (HPS) simulation.

hps2gmx_topol_converter

This program aims to generate the topology file in GROMACS format to use GROMACS built-in analysis program after the implementation of HydroPathy Scale (HPS) simulation.

The HPS parameters of amino acids used in this program are from here, and the ones of nucleotides are from here.

Preparation

This program have to read the HPS topololgy information to generate the GROMACS topology file, thus the HPS topology information should be provided in the following format.

## Starting of the topology information ##  
## Any information about the simulation. ##  
types   <type_number>    # type_number is the total number of the bead types, e.g., 23  
<a list of all the types>    
# Amino acids are represented by uppercase one letter. If the amino acid is at 
# N/C-terminal, "N/C" have to be appended after the one-letter representation. In 
# addition, nucleotides of RNA are represented by lowercase one letter, and "5" 
# should be appended after the nucleotide at 5'-terminal. For instance, 
# Y  MC  NN  S  R  P  W  Q  G  D  F  E  A  K  I  N  L  M  g  u  c  a  g5  

atom   <atom_number>  
# index name mass  charge  
<list of all atoms (beads), zero-based indexing>  
# e.g., 0   NN 114.10    1  
#       1    R 156.20    1  
.  
.  
.  
  
pbonds   <total bond number of amino acids>  
rbonds   <total bond number of nucleotides>  
bonds    <total bond number>  
<list of all bonds between two atoms (beads), zero-based indexing>  
# e.g., 0       1  
#       1       2  
.  
.  
.  
  
## End of the topology information ##  

Dependency

This program has dependency on "cython" package, thus it should be installed before using this program.
pip install cython can be used to install it. If you have installed conda, you can also use the command: conda install cython .

Installation

Turn to your working directory, i.e., cd ...
Give the setup file executable permission, i.e., chmod u+x setup .
After that, it can be easily installed by typing in your console: ./setup build_ext --inplace .

Usage

Give the run_converter file executable permission as well, i.e., chmod u+x run_converter .
The uasge is also very convenient. Just type ./run_converter -hps /input/path/to/your/hps_topology/file -topol /output/path/to/your/gromacs/topol/file .

If your topology information filename is "hps_topol.txt" and the GROMACS topology filename is expected to be "topol.top", just run ./run_converter !

Hope you enjoy it!

If you encounter any problem when using it, feel free to contact me!
E-mail: [email protected]