From: Raul Araya (
Date: Tue May 29 2007 - 16:46:49 CDT

Hi all:

Im working with some pqr files made with the PDB2PQR standalone program.
When I try to look and analyse those file on VMD a lot of errors occurs.
                  an example line of my pqr file look like this:
ATOM 17 HG12 ILE A 1 20.996 48.719 37.539 0.0900 1.3200

The molecules Im using are multi-chain and I kept the chain on the PQR file

and the errors I get from VMD are like this:
1) Warning> Unusual bond between residues 270 <none> and 271 <protein>
2) The molecule look REALLY distorted on VMD (like a fiber of weird atoms)

Also if I changje the name of one of this pqr file to a pdb one the molecule
looks OK but If i try to put a surface on it, the resulting surface is
incomplete, only a part of the molecule surface is drawn.

What can be causing these? What am I doing wrong??
Please help...
Attached is one of my pqr files

Raul Araya
Universidad de Chile

  • application/octet-stream attachment: Wt_70.pqr