AMBER Archive (2004)

Subject: Re: AMBER: how to deal with the initial structure?

From: Furse, Kristina Elisabet (
Date: Tue Aug 24 2004 - 14:29:39 CDT


I considered doing what you suggest last year, but had trouble finding a good
enough way to hydrate the empty cavity left upon removal of the ligand (or in
fact, whether to hydrate it at all...), so other projects took precedence. My
cavity was quite hydrophobic, but technically solvent accessible. It was not
filled automatically when I built a periodic box in leap, but I could use the
solvent cap facility of leap by setting the center of the cap in the center of
the cavity with a radius bigger than the cavity, but not large enough to reach
the exterior of the protein (just used this to place the waters, didn't restrain
them like a real cap). Then I built the periodic box around the whole system.
The water still looked a little sparse and odd in the ligand cavity, so I also
tried Dowser (Jan Hermans--I believe it is freeware). Dowser will place waters
then test to see if the positions are energetically favorable in deciding wheter
or not to keep them. This works quite well for many systems, but my cavity was a
bit too large and hydrophobic to handle that way, so I only got partial
hydration. One more possibility, if I remember correctly..., would be a grand
cannonical simulation, where N is not held constant so waters can appear and
disappear (I'm blanking on the lit reference at the moment). Running that for a
while could potentially fill your cavity if it should be filled. Quite time
intensive, though, so it all depends on how much time and energy you'd like to
throw at the question!

Good luck,

Quoting hj zou <>:

> Dear amber usersúČ
> I'm performing a long-timescale simulation on a protein-ligand
> complex.And now I wanna compare the differences between apo- and holo-
> system.However,no crystal structure of apoprotein is available so far.So I
> wanna delete the ligand of holo-protein,take it as the initial structure of
> apoprotein and then perform a long-time simulation.Can anyone tell me whether
> it's reasonable or not? Any other suggestions?
> Thank you in advance.
> Best regards
> hjzou
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Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
Email: kristina.e.furse_at_Vanderbilt.Edu
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