How to rejoin a separated 2 chain protein after gromacs production run?

02 February 2020 1 9K Report

I want to know how to fix the separation of 2 chains after the production run. I'm trying different combinations of trajconv after creating an index file having a specific residue(s) on the interface between the 2 chains, but nothing is working. I fixed this issue before but when there was only one chain, now with 2 chains, I don't know how to rejoin them together again. Can you suggest me any solution, please?!

*N.B: the 2 chains are considered as one when selected in VMD

Martiniano Bello

Hi Marwa,

If you want to join them numerically or by chain type, this command line will help you.

gmx editconf -f file-in -o file-out -resnr -label

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