I am seeking a way to obtain the contact map between two chains in a protein post MD simulation in gromacs. The objective is to analyze and know which residues in two chains are important during MD.
gmx mdmat
https://manual.gromacs.org/archive/5.0.3/programs/gmx-mdmat.html
Dear Martin Klvana
Thanks point gmx mdmat program. I want to investigate contacts between residues in chain A and chain B during MD simulation. I am not sure how to use gmx mdmat program as it chooses only a single group from index file. However, after choosing protein (group 1) from index file I could generate contact map for all residues in a protein. If I split chains and choose any chain from such index file I get contact map for that chain. I may be missing something very obvious but could you please help sort out this problem?
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