From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Mar 30 2012 - 11:30:08 CDT
The issue is probably the six-character residue type messing up VMD's
column-based psf reader. The standard psfgen writepsf command falls back
to space-delimited in this case to avoid truncation but doesn't include
the very new "NAMD" flag because I didn't want to risk breaking code that
works for everything else. To get the NAMD flag, use the psfgen from NAMD
2.9b2 and use "writemol psf <filename>" instead of writepsf. The writemol
and readmol commands use the VMD molfile plugins, which are (ironically)
not available in the psfgen module incorporated into VMD.
A simpler method is to just rename the residue type in the param file.
-Jim
On Fri, 30 Mar 2012, Massimiliano Porrini wrote:
> 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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