CHARMM GUI online does a protein-protein interaction where you can measure the interaction energy of one chain with all the others. Is there a way to do this for each residue? Basically I want to know what happens to my model if I mutate one residue to another and there are hundreds of these I need to check. So I have to find an automated way.
A lot of programs can do this. For instance, in AMBER the cpptraj tool can calculate the interaction energy with a simple command line. The mdtraj lib for python could also do this calculation....
You can use GROMACS command, gmx energy to calculate energies (such as total energy or LJ or electrostatic interaction energy) between residues or groups of your choice. You have to provide, most importantly, an index file, which defines your groups according to your preference. You can also refer to the documentation for more details: http://manual.gromacs.org/documentation/5.1/onlinehelp/gmx-energy.html
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