Re: PDB sugar unit residue name

From: Massimiliano Porrini (
Date: Thu Mar 29 2012 - 14:05:04 CDT

Hi all,

Thanks a lot for all the replies to my email.
I have tried to upload the psf first and then the pdb, but no luck yet:
still the structure is "messy".

Dear Vincent,

The names in the psf file have not been truncated and I have just
downloaded and installed VMD-1.9.1, read the release notes and then I
simply added
the "NAMD" keyword in the first line, leaving a blank space just after
the PSF keyword, like this:


But no luck again.

I enclose also my input files (pdb and pgn), so that you might help me
to see if I am doing something wrong here.
To be more precise, I am using the psfgen version come out
with NAMD_2.8_Linux-x86_64-multicore .

Thanks a lot in advance.


Il 29 marzo 2012 14:26, Vincent Leroux <> ha scritto:
> Hi,
> Check your PSF file to see if the atom and residue names have not been
> truncated by psfgen. If so, use VMD v1.9.1.
> If the PSF file appears ok, look for the "NAMD" keyword that should be set
> on the 1st line.
> See release notes here:
> And of course, make sure you load the PSF file first in VMD and then the PDB
> file on top of it. Loading PDB files directly that contain non-peptidic
> residue names and no CONECT records (psfgen do not generate those explicit
> bond definitions since they are in the PSF file already) is a sure way to
> get a lot of mess as a result.
> Regards
> VL
> On 29/03/2012 13:03, 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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