VMD-L Mailing List

From: Adrian E. Roitberg (adrian_at_qtp.ufl.edu)
Date: Wed Apr 17 2002 - 07:59:32 CDT

Hi,

has anyone find that vmd has a different naming convention for H atoms
in proteins than pdb recommends ?
I know there is confusion out there about the naming conventions
(historically due to the pdb having mostly x-ray structures and not NMR
ones).

For Alanine for instance, the 3 H atoms in the beta carbon should be
called 1HB 2HB and 3HB. vmd needs them to be called HB1, HB2 and HB3.

Can anyone from vmd tel me why was it done this way ?
Thanks !!
a. 

-- 
                           Dr. Adrian E. Roitberg
          Quantum Theory Project and Department of Chemistry
University of Florida   	       PHONE 352 392-6972
P.O. Box 118435		               FAX   352 392-8722
Gainesville, FL 32611-8435             Email roitberg_at_qtp.ufl.edu 
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