[MMTK] MMTK: Ready for Prime Time?

Warren DeLano warren@sunesis-pharma.com
Thu, 24 Aug 2000 14:45:24 -0700

MMTK seems like a very promising free/open source platform for molecular
modeling, which could be combined with other free/open source packages,
to form the basis for a truly free and open source molecular modeling
environment centered around Python.  Such an environment could
potentially become the Linux of the computational chemistry/modeling

I'm interested in finding out if (and how many) people are using MMTK
for "production" molecular modeling work, and what their experience has
been.  In playing with the program during the last few days I have been
very impressed with existing capabilities (such as the Amber force-field
and normal mode calculations) but there are still some big holes.  Also,
the conjugate gradient minimizer seems very slow to converge ( in
execution time - not necessarily steps) compared to other mimizers I've

Are there any efforts underway to implement the following features into

- An implicit solvation potential energy function
- Amber force field entries (suitable atom types + cross terms) for
common functional groups found in proteins ligands (chloride,
sulfonamide, various heteroatom rings, etc.)
- Automated type and charge assignment (I've done some work on the
former using Python)
- Additional optimizations (such as not calculating forces between fixed
- A faster CGM.

I realize that some of these are tough problems, but the hope of a
freely available Python based molecular modeling system is a dream that
I would love to help make a reality.

- Warren

Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
3696 Haven Ave., Suite C
Redwood City, CA 94063
(650)-556-8800 fax: (650)-556-8824