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 Tue Sep 25 2012 - 13:00:03 PDT
