VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Apr 17 2002 - 10:26:39 CDT

Hi,

VMD really has no naming convention at all, because it doesn't name
anything: it just uses the names given to it. For example, the atom
names in the the decalanin molecule distributed with VMD come from the
X-PLOR force field. The only sense in which naming is important to VMD
is in recognizing certain key atoms, like the backbone atoms or hydrogens.
For this purpose VMD uses a heuristic based on the atom name, which
should recognize atoms named 1HB just as well as HB1 as being hydrogen.

Confusion about the naming convention is, I think, a big part of the reason
why VMD 'plays dumb' and just tries to use whatever names you give it,
rather than trying to map every atom into a particular set of definitions.

Justin
 
On Wed, Apr 17, 2002 at 08:59:32AM -0400, Adrian E. Roitberg wrote:
> 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
> ==================================================================== 

-- 
Justin Gullingsrud      3111 Beckman Institute
H: (217) 384-4220       I got a million ideas that I ain't even rocked yet...
W: (217) 244-8946       -- Mike D