Ligand is not being moved (rotamers, rotation, translation) at all, despite apparently valid spec #200
Description
In an osprey affinity calculation (design file driven), the ligand is not being altered at all - always in exactly the same position, rotation, and with the same rotamers. The relevant part of the design file is here, and I've enclosed the full design (.yaml) and .frcmod files.
Invocation is: osprey affinity --design LiLac_PCr.pdbf.2flexTSubt6R64.yaml --frcmod PCr.gaff2.frcmod --epsilon 0.95 --max-simultaneous-mutations 1 --save-confs 4 --stability-threshold -1
extra_rotamers: |+2
1
PCR 4 64
C4 N3 P1 O3 # phosphate rotation -62, 2
C2 N1 C1 H1 # methyl rotation 93, 33
N1 C2 C3 O1 # carbonyl rotation -8, 82
C1 N1 C2 C3 # carbonyl relative to methyl 102, 132, 72, 42, -28, -58, -88, -118
-62 93 -8 102
-62 93 -8 132
-62 93 -8 72
-62 93 -8 42
-62 93 -8 -28
-62 93 -8 -58
-62 93 -8 -88
-62 93 -8 -118
2 93 -8 102
2 93 -8 132
2 93 -8 72
2 93 -8 42
2 93 -8 -28
2 93 -8 -58
2 93 -8 -88
2 93 -8 -118
-62 33 -8 102
-62 33 -8 132
-62 33 -8 72
-62 33 -8 42
-62 33 -8 -28
-62 33 -8 -58
-62 33 -8 -88
-62 33 -8 -118
2 33 -8 102
2 33 -8 132
2 33 -8 72
2 33 -8 42
2 33 -8 -28
2 33 -8 -58
2 33 -8 -88
2 33 -8 -118
-62 93 82 102
-62 93 82 132
-62 93 82 72
-62 93 82 42
-62 93 82 -28
-62 93 82 -58
-62 93 82 -88
-62 93 82 -118
2 93 82 102
2 93 82 132
2 93 82 72
2 93 82 42
2 93 82 -28
2 93 82 -58
2 93 82 -88
2 93 82 -118
-62 33 82 102
-62 33 82 132
-62 33 82 72
-62 33 82 42
-62 33 82 -28
-62 33 82 -58
-62 33 82 -88
-62 33 82 -118
2 33 82 102
2 33 82 132
2 33 82 72
2 33 82 42
2 33 82 -28
2 33 82 -58
2 33 82 -88
2 33 82 -118
translate_rotate: true