Is it possible to obtain multiple output structures from a Prime side-chain prediction job?

Yes, it is possible to do this by modifying the input file. Due to the combinatorial search done in this case, it is not recommended to run such a job on more than about 8 residues. The procedure to set up the job and run it is:

1. Set up the job from the GUI, then click Write to write out the job files.
2. Edit the jobname.inp file to set the Prime job type and specify the number of structures:
   
   PRIME_TYPE SIDE_COMBI
NUM_OUTPUT_STRUCT n
   
   where n is the desired number of output structures.
3. Start the job from the command line:
   
   $SCHRODINGER/prime jobanme.inp
   

Below is an example input file, asking for 4 output structures:

STRUCT_FILE multout_sc-pred.mae
JOB_TYPE REFINE
PRIME_TYPE SIDE_COMBI
SELECT pick
RESIDUE_0 A:346
RESIDUE_1 A:349
RESIDUE_2 A:350
RESIDUE_3 A:353
RESIDUE_4 A:383
RESIDUE_5 A:394
RESIDUE_6 A:404
NUM_OUTPUT_STRUCT 4
USE_CRYSTAL_SYMMETRY no
USE_RANDOM_SEED no
SEED 0
EXT_DIEL 80.00
USE_MEMBRANE no
HOST hostname

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