VMD-L Mailing List

From: Ahmet yıldırım (ahmedo047_at_gmail.com)
Date: Wed Nov 06 2013 - 05:57:40 CST

Dear users,

I have a problem about APBS in VMD. There isnt response of this error in
VMD mailing list. I am using Ubuntu 12.1 . There is executable apbs in
path /usr/bin/.

1.) I installed VMD 1.9.1
2.) phy_at_phy:~/Desktop/work$ vmd
3.) File-->New molecule-->Fine
name-->Browse-->/home/phy/Desktop/work/final.pqr
OK and LOAD in the VMD Main window
4.)Extensions → Analysis → APBS electrostatics in the VMD Main window
5.) Edit → Settings in the APBS Tool window
Working Directory: "/usr/tmp"-->Browse-->/home/phy/Desktop/work/
Apbs Location:/usr/bin/apbs
OK
6.) "0" calculation from the "Individual PB calculations (ELEC):" window.
7.) Status: Ready
"Run APBS" in the APBS Tool window.
8.) VMD console window:
.....
 Using "molecular" surface definition;harmonic average smoothing
  Solvent probe radius: 1.400 A
  Temperature: 298.150 K
  Potential to be written to pot.dx
  Solving PDE (see io.mc* for details)...
  Calculating energy (see io.mc* for details)...
  Calculating forces...
  Writing potential to pot-PE0.dx
----------------------------------------
CLEANING UP AND SHUTTING DOWN...
Destroying force arrays.
No energy arrays to destroy.
Destroying multigrid structures.
Destroying 1 molecules
Final memory usage: 0.000 MB total, 668.698 MB high water
Thanks for using APBS!
apbsrun) Cannot access output file /home/phy/Desktop/work/apbs.65693/pot.dx

9.) In new window: Error message: Output file missing or unreadable.

How can I fix this ERROR MESSAGE?

Thanks in advance

Ahmet