Method to (approximately) convert the jac benchmark to desmond: 1. Run tleap -f leap.in, where this is the leap.in file: source leaprc.ff99SB x = loadpdb equil.pdb set x box 62.23 saveamberparm x prmtop7 prmcrd7 quit 2. Run the following jobs to create a cms file: $SCHRODINGER/run amber_prm2cms.py -p prmtop7 -c prmcrd7 -o jac.cms [Note: the desmond manual says that you also have to run the "build_constraints.py" file, but Istvan Kolossvary reports that this is not necessary.] 3. Open up a maestro window, use File -> Import Structures to open the jac.cms file. Then go to Applications -> desmond; load the workspace structure into desmond; set up parameters you want, then select "write" to save the files under "jac_desmond". You can then edit the jac_desmond.cfg file to remove unused blocks, and/or to tweak the input parameters. If you like, you can just edit the jac_desmond.cfg file in this directory, which is a cleaned-up version of one that Maestro created. [Note: it's not yet clear to me what is different between jac.cms and jac_desmond.cms, i.e. what if anything Maestro adds to the cms file.] If you add the following line at the end of the Desmond .cfg file, you'll get a detailed breakdown of timing and function calls. profile = {} 4. To run the benchmark, type: $SCHRODINGER/desmond -HOST gyges -P 1 -c jac_desmond.cfg -in jac_desmond.cms where you substitute "gyges" for some entry in your schrodinger.hosts file in directory $SCHRODINGER.