GROMACS version: 2020.1
GROMACS modification: No
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Hi everyone. I am trying to replicate an homology modeling protocol. Right now, I am in the TM refinement part which is made in GROMACS, but I don’t understand how to perform the following “Distance restraints are applied between the backbone O and i +4 backbone N,with r0 =0.28 nm, r1 =0.30nm and r2 =0.31 nm”.
I read that the “gmx genrestr” command is used for distance restraint, but I don’t know how to use it to do the mentioned step.
Here I attach the protocol link.
Thank you in advance for your help.