PDB sugar unit residue name

From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Thu Mar 29 2012 - 06:03:40 CDT

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.


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 : M.Porrini_at_ed.ac.uk

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