Re: [AMBER] Centering a multimeric protein with solvateOct

From: Jonathan Sheehan <>
Date: Thu, 4 Oct 2012 14:24:29 -0500

Hi all,

Just to follow up on my question about solvateOct from last week
(appended below)-

I wasn't able to find an answer in the archive, and my testing with
LEaP never gave me a truncated octahedral box that had 11 Angstroms of
water around the protein on all sides (even off-center). Because I'm
troubleshooting some instability in this simulation, I decided to play
it safe, and I was able to work around this issue by using solvateBox
instead of solvateOct.

I think this might be a "corner-case" bug in LEaP, which only shows up
when using a large multimeric system. But just in case I received no
replies because the answer is too obvious, or I left out key
information, or didn't pose my question well, I invite anyone to smack
me with the clue-bat at this point. :-)


On Tue, Sep 25, 2012 at 2:39 PM, Jonathan Sheehan
<> wrote:
> When I use this command in LEAP:
> solvateOct my_protein SPCBOX 11
> I naively expect to see at least 11 Angstroms of water between
> my_protein and the nearest box edge. But when I double-check (by
> measuring in PyMOL or VMD), I find some protein atoms within 1-2
> Angstroms of the edge.
> My protein is a large hexamer with 12 (internally-bound) ATPs: 6 X 484
> residues, ~23000 atoms before adding water. If I read the archive
> correctly, solvateOct centers the system on only the first molecule,
> so the hexamer could be off-center within the box (which can cause
> imaging difficulties later, but shouldn't affect the calculation).
> But then, I would guess that the solvent distance on the far side of
> the box (assuming it's correct to go straight across) would make up
> for the deficit. E.g. if it's 10 Angstroms too close on one side, then
> the other side should have the extra 10A, for a total distance of 21A
> between protein and box edge. That did not happen in this case; the
> distance to the opposite face is only 10 Angstroms.
> Unless there's a trick to the tessellation that I'm missing, I think
> this may be a problem.
> I could use solvateBox instead, since the box appears to be nicely
> centered on the protein. But it adds 66063 waters rather than 27288,
> so I'd like to avoid that if possible.
> So, could anyone confirm that I should see 11 Angstroms on both
> opposing sides (or at least that they should sum to 22 if it's
> off-center?). Or, alternatively, reassure me that the periodic imaging
> of the truncated octahedron somehow doesn't require that to be true?
> Many thanks,
> -Jonathan
> Additional Details:
> I'm using Amber12 and AmberTools12.
> I tried "11.0", rather than "11" without a difference.
> I tried performing addions before vs. after solvateOct, without a difference.
> I'm still searching the many posts in the archive on related topics-
> forgive me if I've missed the answer there.

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Received on Thu Oct 04 2012 - 12:30:02 PDT
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