SBMOpenMM: A builder of Structure-Based Models for OpenMM
https://github.com/CompBiochBiophLab/sbm-openmm
Different granularities for the models can be selected as All-heavy-Atom and alpha-carbon representations.
These basic models can also be extended to multi-basin potentials employing more than one input configuration.
Here, shared native contacts are modeled with special Gaussian functions to allow for more than one equilibrium distance.
01 - Coarse grained SBM simulations
02 - Coarse grained SBM simulations
03 - Estimating the folding temperature
04 - Estimating free energy profiles
05 - Setting up a multi-basin SBM
Martini Force Field http://www.cgmartini.nl/index.php
Siruh Force Field http://www.sirahff.com/2012/06/sirah-forcefield.html （can be used to study PTM
"Post-Translational Modifications at the Coarse-Grained Level with the SIRAH Force Field" ）
Genesis residule lelvel coarse-grained force field https://www.r-ccs.riken.jp/labs/cbrt/tutorials2019/tutorial-18-1/
https://github.com/azamat-rizuan/HPS-SS-model
COncentration-dependent COarse-grained MOdel （）
https://github.com/feiglab/cocomo
ff_param = {'ALA': {'mass': 71.079, 'charge': 0.0, 'radius': 0.2845, 'epsilon': 0.41, 'azero': 0.00}, 'ARG': {'mass': 157.197, 'charge': 1.0, 'radius': 0.3567, 'epsilon': 0.40, 'azero': 0.05}, 'ASN': {'mass': 114.104, 'charge': 0.0, 'radius': 0.3150, 'epsilon': 0.40, 'azero': 0.05}, 'ASP': {'mass': 114.080, 'charge': -1.0, 'radius': 0.3114, 'epsilon': 0.40, 'azero': 0.05}, 'CYS': {'mass': 103.139, 'charge': 0.0, 'radius': 0.3024, 'epsilon': 0.40, 'azero': 0.05}, 'GLN': {'mass': 128.131, 'charge': 0.0, 'radius': 0.3311, 'epsilon': 0.40, 'azero': 0.05}, 'GLU': {'mass': 128.107, 'charge': -1.0, 'radius': 0.3279, 'epsilon': 0.40, 'azero': 0.05}, 'GLY': {'mass': 57.052, 'charge': 0.0, 'radius': 0.2617, 'epsilon': 0.41, 'azero': 0.00}, 'HIS': {'mass': 137.142, 'charge': 0.0, 'radius': 0.3338, 'epsilon': 0.40, 'azero': 0.05}, 'ILE': {'mass': 113.160, 'charge': 0.0, 'radius': 0.3360, 'epsilon': 0.41, 'azero': 0.00}, 'LEU': {'mass': 113.160, 'charge': 0.0, 'radius': 0.3363, 'epsilon': 0.41, 'azero': 0.00}, 'LYS': {'mass': 129.183, 'charge': 1.0, 'radius': 0.3439, 'epsilon': 0.40, 'azero': 0.05}, 'MET': {'mass': 131.193, 'charge': 0.0, 'radius': 0.3381, 'epsilon': 0.41, 'azero': 0.00}, 'PHE': {'mass': 147.177, 'charge': 0.0, 'radius': 0.3556, 'epsilon': 0.41, 'azero': 0.00}, 'PRO': {'mass': 98.125, 'charge': 0.0, 'radius': 0.3187, 'epsilon': 0.41, 'azero': 0.00}, 'SER': {'mass': 87.078, 'charge': 0.0, 'radius': 0.2927, 'epsilon': 0.40, 'azero': 0.05}, 'THR': {'mass': 101.105, 'charge': 0.0, 'radius': 0.3108, 'epsilon': 0.40, 'azero': 0.05}, 'TRP': {'mass': 186.214, 'charge': 0.0, 'radius': 0.3754, 'epsilon': 0.41, 'azero': 0.00}, 'TYR': {'mass': 163.176, 'charge': 0.0, 'radius': 0.3611, 'epsilon': 0.41, 'azero': 0.00}, 'VAL': {'mass': 99.133, 'charge': 0.0, 'radius': 0.3205, 'epsilon': 0.41, 'azero': 0.00}, 'ADE': {'mass': 315.697, 'charge': -1.0, 'radius': 0.4220, 'epsilon': 0.41, 'azero': 0.05}, 'CYT': {'mass': 305.200, 'charge': -1.0, 'radius': 0.4110, 'epsilon': 0.41, 'azero': 0.05}, 'GUA': {'mass': 345.200, 'charge': -1.0, 'radius': 0.4255, 'epsilon': 0.41, 'azero': 0.05}, 'URA': {'mass': 305.162, 'charge': -1.0, 'radius': 0.4090, 'epsilon': 0.41, 'azero': 0.05}}
Complexes consists of two separate programs: https://github.com/bio-phys/complexespp
Backmapping