Re: PDB sugar unit residue name

From: Michelle Kuttel (
Date: Thu Mar 29 2012 - 09:30:25 CDT

Hi Massimiliano

This is a pretty general solution, so I hope it helps.
I have found with psfgen, that, after generating the structures with the correct patch, the following commands help:

regenerate angles dihedrals

You could also use our "CarbBuilder" program, but it does not yet support all residues and is still under development.
"CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation", Michelle Kuttel, Yue Mao, GĻoran Widmalm and Magnus Lundborg, Proceedings
of the 7th IEEE International Conference on e-Science, pages: 395-402. (paper available from my webiste)

I hope this helps.

Best of luck,

Michelle Kuttel
PH: +27 21 6505107

On 29 Mar 2012, at 1:03 PM, 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 :

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