From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Thu Mar 29 2012 - 17:09:39 CDT
Please test the psfgen from NAMD 2.9b2.
Also, don't put quotes around NAMD in the psf file header.
On Thu, 29 Mar 2012, Massimiliano Porrini wrote:
> 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:
> PSF "NAMD"
> 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 <vincent.leroux_at_loria.fr> ha scritto:
>> 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.
>> 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.
> 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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