modeling software advice

Mike Tennant tennant at mh.uk.sbphrd.com
Wed Aug 9 09:11:27 EST 2000


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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