AMBER Archive (2004)

Subject: AMBER: CAP PROTOCOL SIMULATION

From: Obdulia Rabal (mrabal_at_iqs.es)
Date: Tue May 18 2004 - 04:32:29 CDT

Dear all.

Could anybody tell me a good reference or an idea for a protocol to deal
with caps of water and Poisson-Boltzmann ?
I have read Biotin/Streptavidin tutorial, but as far as I have understood it
works with previous versions of amber,
not with amber8 ( it doesn't appear igb = 10).

My basic cuestion is how should I minimize the solvated complex before
molecular dynamics.

Is it better to freeze solute and minimize water separately or should I
directly minimize the entire complex?

Any idea would be appretiated.

Thanks in advance.

Obdulia Rabal

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