Sorry, it should have been:
; restraints for distances
[ intermolecular_interactions ]
[ bonds ]
; ai aj type b0 kb
1610 4650 6 0.25 500
1624 4646 6 0.33 500
579 4646 6 0.33 500
as type 1 generates exclusions, which cannot be used in intermolecular_interactions.
But regarding the simultaneous distance restraints, as far as I understand, that is only required if they contribute to the same NOE signal, and I presume at least one atom would have to be the same in that case. Do you use NOE at all, or are your restraints just to keep the atoms at the correct distance? I don’t think there’d be any problem if you do:
; restraints for distances
[ intermolecular_interactions ]
[ distance_restraints ]
; ai aj type index type’ low up1 up2 fac
1610 4650 1 0 1 0.25 0.25 0.25 500
1624 4646 1 1 1 0.33 0.33 0.33 500
579 4646 1 2 1 0.33 0.33 0.33 500