modeling software advice

Anne Simonson asimonso at
Wed Aug 9 13:07:25 EST 2000

THanks, Mike!  I appreciate your input.

Mike Tennant wrote:

> Hi Anne,
>         you'll probably want to have a look at NAMOT  (
> and NAB ( for building
> and visualising and there are a load of programs aorund for calculating
> interaction energies (CHARMm, AMBER, NAMD. Just do a 'net search on
> these terms and you'll find the relevent sites easily).
>         RNA isn't an easy system to work with computationally due to the large
> charge associated with these systems (also DNA) and the high flexibility
> of the structures. You should read up on energy calculations and
> simulations using solvent and counter-ions and also on techniques
> involving 'particle mesh Ewald summations' (sounds horrid, I know...!).
>         Have fun,
> Mike

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