From: Axel Kohlmeyer (
Date: Tue May 29 2007 - 18:49:38 CDT

On Tue, 29 May 2007, Raul Araya wrote:


the pqr reader in VMD supports only a subset of PDB constructs
(e.g., we recently added CRYST1). so it is very likely, that your
file confused it and you get the results you describe. the PDB
reader in turn will be confused with the data after the residue id.


RA> Hi all:
RA> Im working with some pqr files made with the PDB2PQR standalone program.
RA> When I try to look and analyse those file on VMD a lot of errors occurs.
RA> an example line of my pqr file look like this:
RA> ATOM 17 HG12 ILE A 1 20.996 48.719 37.539 0.0900 1.3200
RA> The molecules Im using are multi-chain and I kept the chain on the PQR file
RA> and the errors I get from VMD are like this:
RA> 1) Warning> Unusual bond between residues 270 <none> and 271 <protein>
RA> 2) The molecule look REALLY distorted on VMD (like a fiber of weird atoms)
RA> Also if I changje the name of one of this pqr file to a pdb one the molecule
RA> looks OK but If i try to put a surface on it, the resulting surface is
RA> incomplete, only a part of the molecule surface is drawn.
RA> What can be causing these? What am I doing wrong??
RA> Please help...
RA> Attached is one of my pqr files
RA> Thanks
RA> Raul Araya
RA> Universidad de Chile

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.