[BiO BB] looking for potentials for molecule simulations
marchywka at hotmail.com
Wed Mar 21 00:21:18 EDT 2007
After someone's suggestion earlier regarding opengl, I went ahead and wrote
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.
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
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.
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