Is there a way of running ConfGen to generate a big pool of conformers for a certain molecule with a distance constraint?

It is not possible to set up a distance constraint directly in the ConfGen panel. However, since ConfGen is using the same command file as MacroModel, there is a workaround that you can try.

First, go to MacroModel → Conformational Search. In the Constraints tab, add in the distance constraint that you are interested in. Click 'Write' to write out the mmod-jobname.com file.

Now, go to the ConfGen panel, set up the desired job, and click 'Write' to generate the confgen-jobname.com file.

Open both .com files in an editor and copy the FXDI line from the MacroModel .com file to the ConfGen .com file. Please make sure that the line is aligned properly and that the FXDI line is below the READ line.

Start the job from command line:

$SCHRODINGER/bmin confgen_jobname

Keywords: distance constraint, conformers, ConfGen

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