1. Extending the Stochastic Titration CpHMD to CHARMM36m
- Author
-
João G. N. Sequeira, Filipe E. P. Rodrigues, Telmo G. D. Silva, Pedro B. P. S. Reis, and Miguel Machuqueiro
- Subjects
Thioredoxins ,Nucleic Acids ,Lipid Bilayers ,Materials Chemistry ,Escherichia coli ,Humans ,Membrane Proteins ,Micrococcal Nuclease ,Muramidase ,Physical and Theoretical Chemistry ,Hydrogen-Ion Concentration ,Molecular Dynamics Simulation ,Surfaces, Coatings and Films - Abstract
The impact of pH on proteins is significant but often neglected in molecular dynamics simulations. Constant-pH Molecular Dynamics (CpHMD) is the state-of-the-art methodology to deal with these effects. However, it still lacks widespread adoption by the scientific community. The stochastic titration CpHMD is one of such methods that, until now, only supported the GROMOS force field family. Here, we extend this method's implementation to include the CHARMM36m force field available in the GROMACS software package. We test this new implementation with a diverse group of proteins, namely, lysozyme, Staphylococcal nuclease, and human and
- Published
- 2022