From: Axel Kohlmeyer (
Date: Mon Mar 09 2009 - 12:08:49 CDT

On Mon, 2009-03-09 at 13:08 +0100, Leonhard Henkes wrote:
> Hey VMD community,
> at the moment I have a small problem with the pdbalias command used by psfgen. I use this command to convert my input.pbd (produced with a program called PEPBUILDER) for the corresponding forcefield.
> It works fine for atomnames that are not beginning with a number. But if the first part of the atomname is a number (e.g. 3HD1) the "pdbalias" doesn't work anymore. I think this is a syntax problem. The code I use is the following:
> pdbalias atom ILE 1HD1 HD11

one alternative would be to load the .pdb file into vmd
and use a script with selections to rename the offending
atoms. there are different naming conventions out there and
i also remember people mentioning scripts to automate those
renames (e.g. with perl).

> maybe you can help me here with my rookie question,
> sincerely Manny Kalavera

so you've been transferred from the DoD to simulations now. ;-)


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.