modeling software advice

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


THanks, Mike!  I appreciate your input.
--Anne

Mike Tennant wrote:

> Hi Anne,
>         you'll probably want to have a look at NAMOT  (http://namot.lanl.gov/)
> and NAB (http://www.scripps.edu/case/casegr-sh-2.2.html) 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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