How do I build a multimeric homology model with Prime using a multi-chain template?
There are two ways in which you can build a multimer in a single run. The first is to set up a job for each chain, and write the input files rather than run the job. Then run bldstruct from the command line, listing all the input files as arguments: $SCHRODINGER/bldstruct chain1.inp chain2.inp … The second is to edit the FASTA file and concatenate the chains of the multimer into a single chain, with some suitable filler between the chains so that they are easy to identify. Then in the Build Structure step, use Set Template Regions to select the appropriate section of the sequence for each chain template, and choose the options that ensure that template junctions are not built and template gaps are not built.
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