GROMACS version: 2021
GROMACS modification: No
I am running. multimer simulation, especially dimer and hexamer (2 and 6 chains). I am using lysozyme in water tutorial but during pdb to gmx it takes the whole protein dimer to be a single chain in gro (the structure is conserved) such that i have to retrive the structure and rename chains manually in pymol, any insight is appreciated?
Good day,
I would look at the .pdb file: if it has the chain ID, GROMACS will assign it.
Then, you may want to index those groups/chains by using
gmx make_ndx -f your_input.pdb -o index.ndx
using “chain A” etc. to save new groups with your chain
another way (if you know the residues of chain A, example from 1 to 200 etc…) is to create an index group using your *.gro file:
call gmx make_ndx and enter in the interactive shell “r 1-200”, then you can change the name
Hope this helps!