Just a follow-up on this, it turns out that the amber to desmond
conversion script takes care of the constraints and it doesn't matter
whether the prmtop file was generated with or without the
FlexibleWater option. There is no need for running the
build_constraints script. Thus it suffices to run
$SCHRODINGER/run amber_prm2cms.py -p prmtop7 -c prmcrd7 -o jacbench.cms
or
$SCHRODINGER/run amber_prm2cms.py -p prmtop7.noflex -c prmcrd7 -o
jacbench_noflex.cms
where 'noflex' is the normal way tleap is used. Both .cms files will
run the same test. There will be a difference between the number of
stretch terms, but they will be constrained anyway.
Another thing, 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 = {}
Istvan
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Received on Wed Jul 28 2010 - 16:30:04 PDT
