Is it possible to include more than one loop to sample in the IFD protocol?

Yes. In the jobname.inp file written out from the GUI, the STAGE PRIME_LOOP block can be copied to include an additional loop to sample. Note, however, that the two jobs will not be run simultaneously, but rather serially, so that the output conformations from the first loop sampling job will be used as input to the second loop sampling job. The job will have to be started from command-line:

$SCHRODINGER/ifd jobname.inp

Keywords: Induced fit, multiple loop sampling

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