AMBER Archive (2007)

Subject: Re: AMBER: Solvation Issues

From: Eddie Men (pckboy_at_gmail.com)
Date: Sat Sep 29 2007 - 01:31:26 CDT

Thanks for the feedback David

For a second (actually a couple of hours :p) I though WHAT IF meant
trial and error, now that I read da paper I gather WHAT IF is a
program, I felt dumb :x

As a gut feeling, do you think protonating only the aminos in my active
site would be enough?. Or shall I change all of hem?.
10 are important, and 40 are out there, in the surface but away from the
sweet core...As I am wary of computations that last forever may be I
should FIX the state of the outer aminos to a given charge, and then use
the algorithm only in the active center residues, etc.

I appreciate anybody else's input in here

Eddie

David Cerutti wrote:
> 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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