[BiO BB] looking for potentials for molecule simulations

Mike Marchywka marchywka at hotmail.com
Wed Mar 21 00:21:18 EDT 2007

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 
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 
or open topics in the area please let me know- I'm kind of looking for 
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 
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 
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 
macromolecules. The C++ STL containers and opengl make everything pretty 
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.


Live Search Maps – find all the local information you need, right when you 
need it. http://maps.live.com/?icid=hmtag2&FORM=MGAC01

More information about the BBB mailing list