AMBER: solvateOct method

From: Cameron Mura <>
Date: Wed, 23 Feb 2005 18:26:19 -0800


I'm wondering if anyone could explain (briefly or in detail!) the method
used by LEaP's "solvateOct" functionality for setting-up truncated
octahedral PBCs? In particular, I'm wondering about the transformations
applied to the solute and how the corners of the cube are shaved off (or
whatever algorithm is used to construct it)??

The reason I ask this is that I get vastly different results in terms of
number of TIP3 waters depending on whether I (a) go from an initial PDB
file to a solvated octahedral box in xleap, using the solvateOct command
w/ a buffer of, say, 10 A, versus (b) set-up and solvate the system
using other software (like VMD and its psfgen utilities) to immerse the
solute in a large cube and then lop off the corners. The difference is
quite large (~13,000 waters from scenario (a) vs ~19,000 from (b)), and
what really peaked my curiosity is that I get a similar discrepancy in
num of waters if I manually construct the box (i.e., route (b)) using
the solute after it's already been reoriented by xleap's solvateOct

Any info. would be greatly appreciated.


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Received on Thu Feb 24 2005 - 02:53:01 PST
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