Re: PDB sugar unit residue name

From: Olgun Guvench (oguvench_at_une.edu)
Date: Thu Mar 29 2012 - 11:14:52 CDT

Massimiliano,

If you load the psf first, and then load the pdb as coordinates for
the psf, you should see all the connectivities as defined in your psf.

-Olgun

-- 
Olgun Guvench, M.D, Ph.D.
Assistant Professor and Vice Chairperson
Department of Pharmaceutical Sciences
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On Thu, Mar 29, 2012 at 10:30 AM, Michelle Kuttel <mkuttel_at_cs.uct.ac.za> wrote:
> Hi Massimiliano
>
> This is a pretty general solution, so I hope it helps.
> I have found with psfgen, that, after generating the structures with the correct patch, the following commands help:
>
> regenerate angles dihedrals
> guesscoord
>
>
> You could also use our "CarbBuilder" program, but it does not yet support all residues and is still under development.
> http://people.cs.uct.ac.za/~mkuttel/downloads.html
> "CarbBuilder: an adjustable tool for building 3D molecular structures of carbohydrates for molecular simulation", Michelle Kuttel, Yue Mao, G矣ran Widmalm and Magnus Lundborg, Proceedings
> of the 7th IEEE International Conference on e-Science, pages: 395-402.  (paper available from my webiste)
>
> I hope this helps.
>
> Best of luck,
> Michelle
>
>
> -----------------------------
> Michelle Kuttel
> mkuttel_at_cs.uct.ac.za
> PH: +27 21 6505107
> -----------------------------
>
>
>
>
> On 29 Mar 2012, at 1:03 PM, 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
>>
>
>

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