From: Axel Kohlmeyer (
Date: Mon Jun 29 2009 - 22:32:22 CDT

On Tue, 2009-06-30 at 10:59 +0800, accomp lin wrote:

dear jiaqi,

your statement is not correct.

VMD internally supports almost arbitrarily long names.
the molfile API (which is used to read and write files)
supports atom names of up 15 characters.

the limitation you experience lies in the .pdb/.psf
file formats and not in VMD.

also there is generally no need to label each atom
with an individual name since also the "index" and
"sequential" properties do this.


> Dear everybody,
> I am building my MD system using VMD. There is a large thing in my
> system which contains nearly 20k atoms and I wish to have each atom
> name differently. So I use number to name the atoms. However I found
> VMD does not support atom name which have more than four characters,
> e.g. an atom has a name of 14509 will turn out to be 1450 when write
> into psf and pdb. Can VMD be tuned to support long atom name or is
> there any alternative to my problem?
> any help will be appreciated.
> Jiaqi
> ______________________________________________________________________
> 好玩贺卡等你发,邮箱贺卡全新上线!

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.