Re: PDB sugar unit residue name

From: Massimiliano Porrini (M.Porrini_at_ed.ac.uk)
Date: Fri Mar 30 2012 - 07:06:15 CDT

Sorry, here are the files.

Cheers,

Il 30 marzo 2012 13:03, Massimiliano Porrini <M.Porrini_at_ed.ac.uk> ha scritto:
> Dear Vincent,
>
> I have tried with
>
> PSF NAMD
>
> and
>
> PSF NAMD CMAP
>
> and both did not work.
>
> I've also tried to load it from VMD command line and no luck again.
>
>
> Yes, with regard to the procedure, I upload the psf file first and
> then I upload the pdb file in it
> (without calling a New Molecule), but it does not work.
>
> If you are willing to have a go, I enclose my very small sugar
> molecule I am working with
> and the very small pgn file I am using, so that I can understand if I
> am making any error
> in the procedure (especially with the commands in the pgn file, even
> though I doubt,
> as the psfgen execution is smooth).
>
> Regards,
>
>
> Il 30 marzo 2012 12:40, Vincent Leroux <vincent.leroux_at_loria.fr> ha scritto:
>> Regarding the "long atom types tag" the PSF 1st line should look like
>>
>> PSF NAMD
>>
>> without the ""
>>
>> and
>>
>> PSF NAMD CMAP
>>
>> if you use the CMAP version of CHARMM22
>>
>> If you use the VMD GUI you have to load the PSF as "New molecule" then
>> inject PDB data into it (not load the PDB as "New molecule" too). The 1st
>> option of the "Molecule File Browser" is "Load files for:" - this should be
>> set to the previously-loaded PSF when you load the PDB
>>
>> You can also try using the command from the VMD terminal:
>>
>> mol load psf yourpsf.psf pdb yourpdb.pdb
>>
>> If that does not work inspect your files carefully, because there is
>> probably something wrong with them...
>>
>> Regards
>> VL
>>
>>
>>
>> On 29/03/2012 21:05, 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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