From: Mamoru Yamanishi (
Date: Wed Dec 07 2005 - 21:48:56 CST

Hello John,

Thanks for your advise.

> If you're running one of the recent test versions, I've found
> (and just fixed) a bug in the APBS plugin that caused it not to
> find the radii.dat file that VMD uses to assign radii and charge
> information and generate a .pqr file automatically when it runs the job.
> If you're running one of the recent test versions, try replacing your
> apbsrun.tcl script with the new one I've attached to this email.
> The installed apbsrun script is normally found (On unix machines) in:
> /usr/local/lib/vmd/plugins/noarch/tcl/apbsrun1.1/apbsrun.tcl
> Rename the old one to apbsrun.bak and then copy in the new one and
> try re-running your APBS job.

I tried but it was the same. diff command gave followings:

diff apbsrun.tcl apbsrun.tcl.old
< ## $Id: apbsrun.tcl,v 1.101 2005/12/07 23:02:10 johns Exp $

> ## $Id: apbsrun.tcl,v 1.100 2005/04/28 19:20:26 johns Exp $
<   set datfile [file join $::env(VMDDIR) plugins noarch tcl apbsrun1.1 
>   set datfile [file join $::env(VMDDIR) plugins noarch tcl apbsrun1.0 
Do you think that permition or owner of the file/folder affect the
I have additional silly question.  Using PDB2PQR server, the returned PQR file
has lines for hydrogen atom.  On the other hand, a PQR generated by
VMD (or APBS plugin?) has same lines as PDB file.  If there is no ATOM
line for hydrogen, do I think both potentials are (basically) same?
Mamoru Yamanishi, Ph.D. <>
Research Assistant Professor
Dr. Banerjee's Lab., Biochemistry Department
University of Nebraska-Lincoln