Re: how to simulate sugars

From: Aaron Oakley (
Date: Sun May 27 2007 - 19:19:55 CDT

1-Currently the best one for use with CHARMM-protein
is the CSFF forcefield:

2-To build carbohydrates in psfgen the residues will have
to be aliased or renamed to the CSFF convention. (Is TRE
trehalose? If so, I dont think there is a 1-1 linkage patch in


On 28/05/2007, at 3:21 AM, Richard Casey wrote:

> Hello,
> We're using NAMD for protein-sugar simulations. When using psfgen,
> we get various error messages, often something like "unknown
> residue type TRE", etc. I think we need a topology file that
> includes sugars, is that correct? If so, does anyone know where to
> get such topology files?
> Regards,
> Richard Casey

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:44:45 CST