Re: how to simulate sugars

From: Aaron Oakley (oakley_at_rsc.anu.edu.au)
Date: Sun May 27 2007 - 19:19:55 CDT

1-Currently the best one for use with CHARMM-protein
is the CSFF forcefield:
http://people.cs.uct.ac.za/~mkuttel/downloads.html

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
CSFF).

Aaron++

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
>

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