AMBER Archive (2008)

Subject: RE: AMBER: How to set a ZN atom radius for PB calculations

From: Ray Luo (
Date: Thu May 22 2008 - 15:41:36 CDT

Apparently my answer didn't go through the mailing list filter ... here it
is again ...

> Two questions:
> 1) How do I use leap to set the atom radius for ZN? The
> documentation implies that these radii should be included in the
> prmtop file.

When you ask for a printout of the electrostatic potential, sander
will automatically use the radius definition for the supported
graphics program, i.e., that of pymol. So you're not using the radii
in the prmtop file even if you set radiopt=0. This was enforced in
sander because the PB surface has to be consistent with that of pymol
for proper visualization.

I think the supported atom type for zinc should be "Zn", but not "ZN". So if

you change the "atom type" to "Zn" when you save your prmtop file, it
should work.

> 2) Where is the pbsa.phi file when I set igb=0?

Of course, if you set igb=0, no pb is used, so no "pbsa.phi"

All the best,

Ray Luo, Ph.D.
Associate Professor
Dept Molecular Biology & Biochemistry
University of California, Irvine, CA 92697
USPS: PO Box 3900 Email:
Phones: (949) 824-9528, 9562

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