Re: PDB sugar unit residue name

From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Fri Mar 30 2012 - 04:57:14 CDT

Hi all,

I have just tried using psfgen of NAMD 2.9b2 to generate psf and pdb
files, I have added NAMD keyword (without quotes) at the first line of the
psf file, I have uploaded the psf file and on top of it the pdb file
in VMD-1.9.1
and the structure is still messy :-(

I am afraid I have to do the post-processing work in fixing the pdb and
psf files with a script (as Norman Geist suggested too).
I can't see any error in my procedure and eventually the files are produced
smoothly (has any one tried to use my input files attached in my
previous email?).

By the way, I am wondering if I can add any command in the pgn file in
order to map
the residue names back to those with only three letters, I mean just before my
following commands:

   writepdb aglcna.pdb
   writepsf aglcna.psf

so that I do not have to post-process the files created from psfgen.

Thanks to all for the hints and all the best.
Max

Il 29 marzo 2012 23:09, Jim Phillips <jim_at_ks.uiuc.edu> ha scritto:
>
> Please test the psfgen from NAMD 2.9b2.
>
> Also, don't put quotes around NAMD in the psf file header.
>
> -Jim
>
>
>
> 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.
>>
>> Regards,
>>
>>
>> Il 29 marzo 2012 14:26, Vincent Leroux <vincent.leroux_at_loria.fr> 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:
>>> http://www.ks.uiuc.edu/Research/vmd/current/devel.html
>>>
>>> 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 : M.Porrini_at_ed.ac.uk
>>              mozz76_at_gmail.com
>>              maxp_at_iesl.forth.gr

-- 
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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