From: Jim Parker (
Date: Fri Apr 04 2014 - 05:42:33 CDT

  I am attempting to use ffTK to parameterize a porphyrin molecule. All
works well until I attempt to find the water interaction energy between a
water molecule and the hydrogen on the interior pyrrole units (attached
.pdb with molecule).
  The problem is that the line of interaction defined by the ffTK program
causes the water to be too close to the hydrogen on the other side of the
ring (.gau file attached also). I could arbitrarily rotate the line out of
the plane of the molecule, which would "fix" the "atoms too close" error in
Gaussian, but I don't know what was the guiding principle for choosing the
original line. It appears to be the direction of closest approach to the
molecule from "outside", but how critical the charges rely upon that line I
don't know.
  Bottomline, I can't run as is. What guidance can you give for updating
the .gau file?

I'm using VMD version 1.9.2a35
And have found the screencasts very helpful, but don't address this issue.

  ffTk is a very helpful tool, thanks for your work on this.