[MMTK] Molecular Dynamics Problem

Konrad Hinsen hinsen@cnrs-orleans.fr
Tue, 17 Apr 2001 11:06:41 +0200


> Hello, I'm trying to build a simple Molecular Dynamics simulation using The
> Dna and ligand example in the MMTK2 Example directory. Here is the source
> code:

There's one comment that hints at the problem:

> # Construct the ligand. There is no definition of it in the database,
> # so it can only be constructed as a collection of atoms. The second
> # argument of createMolecules() is set to one in order to allow
> # this use of an unknown residue.

So your ligand isn't known to MMTK, which means that all the
information it has is the chemical elements of the atoms (that's what
you can deduce from the PDB file). That is not enough to calculate
energies or forces, so you cannot run Molecular Dynamics either.

> What am I missing?

A database entry for the ligand. Which is rather easy to write if
you have the force field parameters for the ligand, but these
may not be so easy to find.

Konrad.
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