From: Ajasja Ljubetič (
Date: Wed Jun 13 2012 - 05:41:27 CDT

I just downloaded the CGenFF and browsed the file "top_all36_cgenff.rtf".
It seems that atom names *are *in fact always 4 characters our less. The
atom *types *designations are longer*. *So basically there is no problem. I
apologize for adding noise to the list.

On 13 June 2012 12:33, Ajasja Ljubetič <> wrote:

> Dear All,
> the CGenFF <> is very useful
> for parametrizing small molecules. But since it contains so much data, the
> atom names are longer than four characters. This causes havoc with many
> programs that truncate atom names to 3 or 4 characters (Well actually the PDB
> standard <>allows only four chars for the atom name). My question is:
> How can I prepare a PDB file with for use with psfgen? Will psfgen work
> with parameter sets, that contain atoms with long names?
> There was a related question<>on the namd mailing list a while ago, but nobody answered, so I apologize,
> if I missed something obvious.
> Best Regards,
> Ajasja