AMBER Archive (2007)

Subject: Re: AMBER: Solvation Issues

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Sat Sep 29 2007 - 22:55:43 CDT

No, use the program for the entire protein. It will probably not be very
difficult to assign protonation states to surface residues. But,
semi-buried things are much trickier. If you think there's room for
debate as to the protonation states of various residues, you might also
consider picking a handful of alternate combinations of protonation states
for the active site, to see if they give you different results. It's
possible that some proteins have protonation states that aren't the
dominant states but are nonetheless the catalytic states.

Dave

On Sat, 29 Sep 2007, Eddie Men wrote:

> 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
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