VMD-L Mailing List

From: Leonardo G. Trabuco (ltrabuco_at_ks.uiuc.edu)
Date: Wed Apr 05 2006 - 22:08:02 CDT

On Tue, Apr 04, 2006 at 06:17:17PM -0400, Margaret Shun Cheung wrote:
> Dear VMD wizards,
>
> I tried to generate psf from a pdb structure. It gave me warning messages
> on N-, and C- residues when I run the script:
>
> Warning: poorly guessed coordinate for atom HT1 ....
> Warning: poorly guessed coordinate for atom HT2 ...
> Warning: poorly guessed coordinate for atom HT3 ..
> Warning: poorly guessed coordinate for atom OT1 ...
> Warning: poorly guessed coordinate for atom OT2 ..

There's a catch here. Psfgen looks for OT1 and OT2 atoms in your
carboxy terminus, but usually a PDB file has them named O and OXT. If
you rename the last two oxygens in your protein from O and OXT to OT1
and OT2, psfgen will not have to guess the coordinates and your
structure will be more accurate.

Usually poorly guessed coordinates for hydrogen atoms are not a reason
for concerns.

Leo 

-- 
Leonardo Giantini Trabuco
Ph.D. student
Center for Biophysics and Computational Biology
University of Illinois at Urbana-Champaign