Re: PDB sugar unit residue name

From: Aron Broom (
Date: Thu Mar 29 2012 - 07:52:20 CDT

Is it possible to use the GLYCAM forcefield instead? It is used with the
AMBER FF, but I've been using the two in NAMD for some time.

On Thu, Mar 29, 2012 at 7:03 AM, Massimiliano Porrini <>wrote:

> Dear all,
> I am experiencing some problems with the CHARMM ff carbohydrates
> residues names in the PDB file created via psfgen.
> I defined some alias names in the pgn file in order
> to map the carbohydrates residue names to those used by CHARMM.
> The pdb (and psf) files are created smoothly so far (with no errors
> and warnings),
> but when I try to display the pdb with VMD I do not get the proper
> structure (VMD just shows an ensemble
> of scattered atoms). As far as I could understand this is because the name
> of the sugar units exceeds the field reserved to the residues name,
> which should be 3 characters
> long according to the PDB format, whilst some sugar names in CHARMM are
> longer (like for instance AGLCNA or AIDOA and so on).
> How could this issue get sorted out?
> As long as the oligosaccharide is relatively small I can do it
> manually (and I did it
> for a test case leaving just the first 3 characters of the residue
> names and VMD displayed
> properly the structure), but with a very long (and branched) sugar
> chain, it becomes harder.
> Any hint would be very appreciated.
> Regards,
> --
> Dr Massimiliano Porrini
> Institute for Condensed Matter and Complex Systems
> School of Physics & Astronomy
> The University of Edinburgh
> James Clerk Maxwell Building
> The King's Buildings
> Mayfield Road
> Edinburgh EH9 3JZ
> Tel +44-(0)131-650-5229
> E-mails :

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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