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

[Anton Feenstra]

Vanja Petrovic wrote:

> 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.

Have you already successfully setup runs for the protein and surface separately?
In general, support for automated topology and conformation generation in
Gromacs is limited to protein in water systems or similar.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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