Using the Amber force field in desmond

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, where this is the file:

    source leaprc.ff99SB
    x = loadpdb equil.pdb
    set x box 62.23
    saveamberparm x prmtop7 prmcrd7

2.  Run the following jobs to create a cms file:

    $SCHRODINGER/run -p prmtop7 -c prmcrd7 -o jac.cms

    [Note: the desmond manual says that you also have to run the
    "" 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

    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.