VMD-L Mailing List

From: Rodrigo Silveira (rodrigolsilveira_at_gmail.com)
Date: Sat Apr 17 2010 - 14:33:58 CDT

Knut,

When a PQR file is loaded into VMD, bond distances are inferred from the PQR
radii. These radii were chosen for continuum electrostatics calculations,
not visualization, and therefore some of the radii are artificially small.
Don't worry if some of the bonds appear a bit strange. 

-- 
Rodrigo
2010/4/17 Knut Jørgen Bjuland <knutjorgen_at_gmail.com>
> When I use vmd to view pqr files with include chain from a polypetid vmd
> can not show the file correct. I have seen the file correct in pymol. I used
> pdb2pqr to add charge to a ph=8.5. For my experiment I used 2OB0.
>
> Knut J
>