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 University of New England College of Pharmacy 716 Stevens Avenue, Room 317 Portland, Maine 04103 207-221-4171 fax 207-523-1926 oguvench_at_une.edu 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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