[BiO BB] looking for potentials for molecule simulations

[Mike Marchywka]

Hi,
After someone's suggestion earlier regarding opengl, I went ahead and wrote 
a molecule
viewer ( details below). I tested some modelling concepts using a simple
1/r potential and wanted to find some options for more realistic 
simulations.
Anyone know off hand of particularly realistic model potentials, preferably
only with parameters that can be derived from a pdb file :)

I originally thought the interesting thing was going to be cavity modelling-
all I've seen in this area is O. If anyone has a link to some nice cavity 
pictures
or open topics in the area please let me know- I'm kind of looking for 
something
useful to do with this code now :) The cavity outlines I've produced so far 
see to be
accurate but lacking in any obvious usage. I was curious to see if I could 
characterize
the active site of an enzyme well enough to get some idea of selectivity. 
Right now
I just have pictures- some visually appealing but of no obvious use yet.

And, yes, I did check google first but as you can imagine it is a big 
area...
http://en.wikipedia.org/wiki/Molecular_dynamics
The above does list pymol, I guess  I could lift some of their code even if 
I can't get
the whole thing to build.




fwiw, a few details:
I wrote an opengl molecule viewer using C++-. I was able to
display and outline the inner cavity for a proteasome and manipulate some 
other
macromolecules. The C++ STL containers and opengl make everything pretty 
easy.
I won't claim it has as many niceties as RasMol yet, but the data structures 
should give
me some flexibility for later. I originally ddn't think it would be worth 
the effort but I couldn't
immediately get pymol to build under cygwin so I thought I would give it a 
try and now
think it may be worthwhile.

Thanks.

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