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Article ID: 305 - Last Modified:

There is a loop close to the active site of my system. Can I sample it as part of the IFD protocol?

Yes. Set up the IFD job from the GUI, then choose to write out the job files rather than to start the job. In the jobname.inp file, there is a commented out block titled "STAGE PRIME_LOOP". Uncomment the lines of this block by removing the # signs and modify the start and end residue numbers to reflect the loop that you wish to be sampled. Then, start the IFD job from the command line as follows:

$SCHRODINGER/ifd jobname.inp

Keywords: Induced fit, loop sampling, prediction

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