AMBER Archive (2007)

Subject: Re: AMBER: Solvation Issues

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Wed Sep 26 2007 - 18:53:11 CDT

Hi Eddie,

    If your protein is larger than about 100 amino acids, you should
seriously consider just using explicit solvent for the entirety of the
calculation. This will be both computationally faster and more realistic
than the system you're describing. If you want to do QM/MM calculations,
then as I understand it the quantum portion of the system will likely take
up the bulk of your calculation no matter what you do.
    For constant pH, you should probably simply protonate the side-chains
of particular amino acids as appropriate for simulations at your desired
pH (WHATIF is frequently used for this), but if you want to use the AMBER
constant pH features then pure Generalized Born implementations are
available in SANDER for this purpose.

Dave
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