[gmx-users] how to write the correct top file for membraneprotein system?

Mark Abraham mark.abraham at anu.edu.au
Sun Nov 25 13:59:58 CET 2007

> Hi Liang,
> Do you have to define ffoplsaa.itp in your top file? isn't it enough to
> generate your protein topology with the OPLS forcefield using pdb2gmx and
> include the protein's generated itp files?

No, because the .itp file is not self-contained. It is a topology for use
with a particular forcefield, and requires the ability to look up values
like atom types that are defined for that force field. This is a *good
thing* because it inhibits people from mixing and matching forcefields for
different parts of their system.


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