VMD-L Mailing List

From: Grant Schauer (grantschauer_at_gmail.com)
Date: Thu May 12 2011 - 13:16:46 CDT

Hello all,

I'm trying to solvate a small system consisting of a small peptide patched
to a novel residue built from CGenFF definitions. When I attempt to
autoionize the system after solvating, I get a warning that I have a
non-integer charge. In fact, it's measuring +67.08000009506941e.

I get the same number with the following commands (regardless of whether
it's solvated):

set sel [atomselect top all]
set charge [vecsum [$sel get charge]]

But when I add up the charges from the PSF by hand, I get exactly the
integer (+2) that I expect, as specified in my topology file. Autopsf runs
smoothly, with no complaints that I'm seeing. I'm running VMD 1.9.

Any suggestions? Thanks,
Grant