The Desmond Users' Manual has instructions on converting Amber prmtop files to Maestro/Desmond format. As a small addition to that, here are some notes on how to convert the "jac" benchmark:
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.