Hello,
I am trying to apply a restraint between an atom in my ligand (atom number 12) and an atom in the active site of my protein (atom number 582) in GROMACS.
I have modified the [ bonds ] section in the topol.top (see attached) so it now reads:
[ bonds ]
; ai aj funct c0 c1 c2 c3
12 582 6 0.25 5e+05
I believe this should restrain atoms 12 and 582 with a type 6 bond restraint, at a distance of 0.25 nm, and a force constant of some multiple of 5e+05.
However, it seems that the simulation entirely ignores this distance restraint and the ligand begins to move away from the active site to a distance of 10 Angstroms or more.
Any help with this is gratefully received.
Hi, I think you need position restraints rather than a bond here (though you can create a bond between ligand and protein atoms that needs extra things).
For adding restraint, you can follow this template:
https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html
Please following the "Using distance restraints" at this:
https://manual.gromacs.org/current/reference-manual/functions/restraints.html
here, the example is about the NMR distance restraints, but you can modify it to suite your need.
This "harmonic restraints: use [ bonds ] type 6" refers to the type of bond that you need to use while defining the restrains.
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