How to create a contact map between an especific aminoacids group?

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1

GROMACS version: 2020.4
GROMACS modification: No
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Hi everyone i have a gromacs trajectory and i want to create a contact map for some specific aminoacid in a region of my protein. Anyone can tell me how i can do this?
Thanks a lot.

2

Hi Mario,

you can have a go with gmx mindist which tells you if things were in contact or not.

If you’re not afraid of compiling some old code, you can have a try with g_contacts which has an option to give you per-residue contact frequencies (read more here ;) )

3

I have gromacs 2019.4
I’m trying to use mindist but i don’t understand how to insert the data to do this analysis. Can you tell me if i need to insert an index?
The index is for an especific atom or can be an aminoacid residue?
Thanks for your help.