SGCMC ensemble to generate different protonated microestates for a given protein.
Authors: Sergio Madurga, Haruna Luz Barazorda-Ccahuana
This program calculates the protonation and deprotonation states by Semi-Grand Canonical Monte Carlo (SGCMC) procedure based on the free energy associated with the pKa of each titratable residue.
A defined number of protonation/deprotonation steps are carried out to generate different uncorrelated microestates compatible with a determined pH.
The program uses the predicted pKa values of a protein using the output format of PROPKA v3.
Citation: Barazorda-Ccahuana, H.L.; Nedyalkova, M.; Mas, F.; Madurga, S. Unveiling the Effect of Low pH on the SARS-CoV-2 Main Protease by Molecular Dynamics Simulations. Polymers 2021, 13, 3823. https://doi.org/10.3390/polym13213823