From: Nicholas Musolino (
Date: Sun Jun 20 2010 - 20:23:50 CDT

You could try writing a script in AWK, a text processing language. You could use it's associative arrays feature, and the program would be pretty simple.

BUT, if your real problem is that the PDB format can't handle your (unique) atom names because of the character limit that Axel mentioned, then all the text-editting cleverness in the world won't help.

I've attached a sample AWK script (UNIX plain text format) that I use to assign unique atom names to MOL2 files. You could use it as a starting point and modify it for PDB format (e.g. change what lines it acts on, the output format, etc).

If you have any specific questions about it you could e-mail me off-list, but please do try to look up the AWK line-based programming paradigm and programming issues yourself first.

Good luck!

Nicholas Musolino

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