[MMTK] PDB reading

[Peter]

mprabha at fiu.edu wrote:
> I could not be able to load any pdb even single peptide. 
> Do you have any script of loading PDB and doing simulation please forward it to me
> thank you
> Prabhakaran

I have been able to load most PDB files I have tried, but have not tried 
any simulations with them.

There should be some examples included with MMTK (if you are on windows, 
you will need to download the full source distribution as the examples 
are not included in the windows installer).

http://dirac.cnrs-orleans.fr/mmtk_wiki/ExampleScripts
http://starship.python.net/crew/hinsen/MMTK/examples.html

In particular, look at:

http://starship.python.net/crew/hinsen/MMTK/Manual/Examples/Miscellaneous/construct_from_pdb.py.html
http://starship.python.net/crew/hinsen/MMTK/Manual/Examples/Proteins/analysis.py.html
http://starship.python.net/crew/hinsen/MMTK/Manual/Examples/Proteins/construction.py.html

(The last example might help with my current problem recently posted to 
the list, by reading a file with hydrogens and creating a structure 
without them)

Peter