This is probably ambitious, but I'd like to use AMBER to simulate
protein unfolding, and possibly refolding. Initially, I thought that it
would be best to do this in (explicit) water, but now I am worried that
the solvent will blow up if I heat it much too much. The generalized Born
solvent model looks more attractive in terms of computational time, but
may not be accurate enough for folding studies. Does anyone have
experience in using AMBER for folding simulations? I'd appreciate any
advice people might have about clever tricks to try and pitfalls to avoid.
Thanks,
Elizabeth White
Received on Thu Jun 28 2001 - 14:52:19 PDT
