VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed Jun 13 2012 - 05:33:27 CDT

Dear All,

the CGenFF <http://mackerell.umaryland.edu/~kenno/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 <http://www.wwpdb.org/documentation/format32/sect9.html#ATOM>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<http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2011-2012/0264.html>on
the namd mailing list a while ago, but nobody answered, so I
apologize,
if I missed something obvious.

Best Regards,
Ajasja