From: Timothy Isgro (
Date: Wed Jun 14 2006 - 15:13:22 CDT

Hi Prashanth,

On Jun 14, 2006, at 9:05 AM, Prashanth Athri wrote:

> Dear "Tutorial Publishers":
> There have been appx. 3 questions on ligand-biopolymer interactions
> on the main archive. I think a Protein-ligand molecular dynamics
> simulation example would be of great benefit to all i.e. two non-
> bonded molecules.

Thanks for the feedback. We will certainly keep this in mind when
thinking of new tutorials for development.

> As far as previously published tutorials, what would be the best
> guide for building parameterisation of a completly new small molecule?

Two tutorials come to mind. "Parameterizing a Novel Residue" will
guide you in calculating parameters for a new molecule. "Topology
File Tutorial" will guide you in making the Charmm topology and
parameter files for a new molecule which resembles another, already
parameterized molecule. The files are made by analogizing to the old

They can be found here under "Science Topics":

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