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 =0.30 nm 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.
Thank you in advance for your help.
Hi,
you have all information on Gromacs Manual:
https://manual.gromacs.org/documentation/2019/reference-manual/functions/restraints.html
However, you cannot do that directly with "gmx genrestr" unless you have an index with the atoms of interest (O and i+4 backbone N) and using "--disre" option.
From the data you have provided, it would be something like:
[ distance_restraints ]
; ai aj type index type' low up1 up2 fac
O i+4_N 1 0 1 0.28 0.3 0.31 1.0
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