cemm-gen 2024.7.23

Cellular Environment Mimicking Model GENerator

Cellular Environment Mimicking Model GENerator

Welcome to CEMM-GEN

What is CEMM-GEN?

CEMM-GEN is a new tool aiming to generate cellular environment mimicking model for molecular dynamics simulation. CEMM-GEN provides a configuration with any modification group added to the spherical or cylinder-like interior.

Requirements

Python >= 3.8, conda, openbabel, psi4, resp, ambertools, scikit-learn, rdkit, parmed

Instllation

conda create -n cemm-gen-env
conda activate cemm-gen-env
conda install -c conda-forge openbabel psi4 resp ambertools
pip install cemm-gen

Basic Usage

# Make a cylindrical model
cemm-gen cylinder --proteinseq GASGASGASGAS --proteinSS HHHHHHHHHHHH --resnames MTY:HYD --composition 1:2.5

# Make a spherical model
cemm-gen sphere --proteinpdb protein.pdb --resnames MTY:HYD --composition 0.3:0.7

# Make parameters for a new residue
cemm-gen makeparam --smiles CCC --resname MTY --description "Methyl group"

Please see the documentation English / 日本語

Version History

See the version history for the latest updates.

Cite Us

T. Yasuda, R. Morita, Y. Shigeta and R. Harada. "Cellular Environment Mimicking Model GENerator: A tool for generating a cellular environment mimicking model."XXXX,2024,XXXX,doi

Authors

Takunori Yasuda, Doctoral Program in Biology, University of Tsukuba Rikuri Morita, Center for Computational Sciences, University of Tsukuba
Yasuteru Shigeta, Center for Computational Sciences, University of Tsukuba
Ryuhei Harada, Center for Computational Sciences, University of Tsukuba
[e-mail]