[gmx-users] model run of a protein against a surface

[Vanja Petrovic]

Hello,
I'm trying to run a simulation of a protein (1PID.pdb) against a model surface (mica or HOPG) for which I also have the .pdb file.  Could someone explain to me how to incorporate the protein and the surface together in a model in order to do mdrun.  Which Gromacs commands do this?  So far I've been trying to build the model by editing the text files manually, but that's really bad, and I haven't been able to find this information in the manual.
Any hints/explanations would be much appreciated.
Thanks

Vanja P.
University of Toronto
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