From: Axel Kohlmeyer (
Date: Sun Jun 20 2010 - 18:55:39 CDT

On Fri, Jun 18, 2010 at 10:19 PM, Moeed <> wrote:
> Hello,
> I wanted to know if vmd can create a pdb file with atom numbering. i.e. for
> example C1, H1..and not as C H N ...


> Actually, I am dealing with a long polymer chain, polyethylene (40000 Mw)
> and to define the residues I need to have atoms numberings so that the
> program recognizes the atoms. Normally softwares that generate structure
> file do not have atoms numbered and to do this by hand is very tedious for
> big molecules.

this cannot work. the pdb standard allows only four characters
for the atom name, so you cannot go beyond C999, H999,
or N999. while VMD can internally handle longer atom names,
the pdb write plugin will always write output in a pdb conforming
format (well mostly, it will skip required fields, if the information
is not present).

> Please guide me what is the best approach to make such a big molecule.

fix your program.


> Thanks
> moeed

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.