Dear all,
I would like to simulate the adsorption behaviour of a protein on an
alumina (0001) surface. I am going to keep the whole slab representing
the oxide substrate fixed throughout the simulation, and I am thinking
of considering it as a single unit in building the input files. I have
already built the .lib files for the Al, O and H atoms, and the
parameters are properly attributed when I load the .pdb file with the
substrate structure into xleap. Would it make sense to just save the
topology and coordinate files for the alumina substrate without
specifying the connectivity, i.e. without defining the bonds inside
the slab, since I want to consider it as a "frozen" object anyway? Or
do I still need to build the bonds inside the structure atom by atom
(or using the bondbydistance command)?
Thank you very much for your kind help!
Giulia
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Received on Sun Sep 05 2010 - 15:30:03 PDT
