GROMACS version: 2022.3
GROMACS modification: Yes/No
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I am new at running FEP and I have recently ran FEP on the dataset provided by
Absolute Binding Free Energy - Gromacs 2016 - AlchemistryWiki. I am not sure as to how we can restrain the ligand? I had a look at the topology file and they have included the following (1 distance, 2 angle, 3 dihedral restraints)
[ intermolecular_interactions]
[ bonds ]
; ai aj type bA kA bB kB
1391 2615 6 0.654 0.0 0.654 4184.0
[ angles ]
; ai aj ak type thA fcA thB fcB
1393 1391 2615 1 88.8 0.0 88.8 41.84
1391 2615 2614 1 32.9 0.0 32.9 41.84
[ dihedrals ]
; ai aj ak al type thA fcA thB fcB
1410 1393 1391 2615 2 -159.7 0.0 -159.7 41.84
1393 1391 2615 2614 2 122.6 0.0 122.6 41.84
1391 2615 2614 2610 2 12.8 0.0 12.8 41.84
I was wondering how can these values be calculated to be included in the topology file.
Best regards,
Kandwal