Egidijus Kuprusevicius wrote:
Hi,
Could anyone tell me how to parameterize a new molecule for using it
with OPLS (basic principles).
See http://wiki.gromacs.org/index.php/Parameterization
> What a .pdb file should look like
As normal, you need atom and residue names corresponding to those for
your forcefield, as modified.
> and what
> .mdp variables are specificaly related to OPLS?
None. That's not what .mdp parameters are for. Roughly speaking, the
.top file and it's #includes define the model of physics for the system,
and the .mdp file controls the choice of algorithms for the simulation.
The two are interdependent, however.
Mark
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