Hi all,
I am new to the molecular dynamics simulation for biomolecules and wanted to asked some questions.
Q1. what are some fundamental differences between AMBER, GROMACS, CHARMM and AMOEBA in their force field parameters?
Q2. I want to simulate a maltose binding protein (not a membrane protein and quite small) to see their transition states between the closed and open forms. What would be a good force field program to use for this given their differences at the fundamental level? If necessary, I could think about introduce one mutant to slow down the dynamics a bit.
Thanks!
Cece
Hi...
A1 Different research groups develop different force fields employing different level of quantum chemistry calculations. These force fields are based on certain experimental data and that’s why most of the force field differs. Like GROMACS is for protein, AMBER is for nucleic acid, AMBER and CHARMM parameters take care of amino acid backbone and side chain dihedrals and different force field treat water model in different pattern and so on. It is better not to mix these force field parameters.
A2 First look for literature if some one has already used force field on the same protein.
The articles for respective force field is the first step you have to do, have a look on few kinds of literature about the developments of the force field and parameterisation of molecules.
Later, you can have small simulations with the same system but in a different force field, which help you to get an understanding about the FF.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology