Can I set up the ligand features for constraints in the Glide input file?

Yes, you can add lines to the jobname.in file to set up the constraints. For example, for the SP docking with constraints job from the Quick Start Guide, you could add the following lines to the input file:

[ FEATURE:1 ]
PATTERN1 [a] 1
[ FEATURE:2 ]
PATTERN1 [H][N,n] 1
PATTERN2 [H][S;X2] 1
PATTERN3 [H][O-] 1
PATTERN4 [H][O;X2] 1
[ CONSTRAINT_GROUP:1 ]
USE_CONS S4_arom:1 S1_site:2
NREQUIRED_CONS ALL

These lines will be used to generate the necessary .feat file at runtime. Note that the index after the colon in the FEATURE:n label must match the index after the constraint_name: on the USE_CONS line.

Keywords: Glide, constraints, input file

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