How to get the contact map between two protein chains from gromacs trajectories?

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09 February 2021 7,086 8 View

OmniScriptum Publishing Group?

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Could you please suggest 3D opensource plotting tool for spheres, cylinders and other shapes?

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Following is XRD of iron oxide nano material synthesised using bipyridine derivatives. What are the reasons for Broad Humps?

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How to analyze a particular region of my simulation box in GROMACS?

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26 February 2021 10,014 3 View

How does GROMACS calculate the average structure of proteins?

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How to identify or create correct list from GROMACS options during analysis of trajectory ?

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20 February 2021 1,750 1 View

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Dr Rajesh B Patil

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?