From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Thu Mar 29 2012 - 14:05:04 CDT
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".
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
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 <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 mozz76_at_gmail.com maxp_at_iesl.forth.gr
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