HyresBuilder: A simple package for building HyRes model.

This package is forked from PeptideBuilder and we do some modifications for HyRes.
Thanks for the contribution of PeptideBuilder.
Shanlong Li

Installation:

dependencies:

git clone https://github.com/lslumass/HyresBuilder.git
python setup.py install

Basic usage:

This package builds HyRes peptide structure from sequence.
Please follow the examples for details of the script and sequence files.

for a single sequence:

Take tdp_43 as an example, to create HyRes tdp_43, one can just run:
python simple_example.py tdp-43-lcd.seq tdp-43_hyres.pdb

for a set of sequences:

To quickly build a series of peptides, one can use:
python bactch_example.py idps.seq
the first line in idps.seq gives the peptide names (also used as the pdb file name), and then the sequence following.

then:

To obtain psf file and further run simulation on OpenMM, please follow these instructions.

Note

After obtaining the pdb files, the initial structures need to be relaxed to get more reasonable state.

Modules:

Module 1: HyresBuilder
build Hyres protein model

Module 2: RNAbuilder
build RNA CG model

Module 3: HyresFF
create hyres system in OpenMM