There appear to be TER cards between the oligosaccharide branches in the
PDB file. This is good, but you probably need to issue explicit 'bond'
commands to re-link the branches when you load the file into leap,
depending on how you made the pdb. This is a workaround for limitations in
PDB format.
Please write to the GLYCAM-L list or post a bug if you have problems with
the website.
GLYCAM-L: https://listserv.uga.edu/cgi-bin/wa?A0=GLYCAM-L
Bug reports: http://glycam.org/bugz
On Wed, Mar 29, 2017 at 8:32 AM, Manju Sah <manjusah.gmail.com> wrote:
> Thankyou for the suggestion.
>
> I tried with the oligosaccharide generated using Glycan builder.
> Then I performed vaccum and solvent minimization. After vaccum minimization
> the branched linkage is intact, but after solvent minimization the branched
> linkage is broken and as well as one ring opening was present.
>
> Now it looks like the problem is not with oligosaccharide building but with
> the forcefield mapping.
>
> Thankyou
>
> Manju
>
> On Wed, Mar 29, 2017 at 5:27 PM, David Case <david.case.rutgers.edu>
> wrote:
>
> > On Wed, Mar 29, 2017, Sangeetha B wrote:
> > >
> > > I also tried the glycam.org website to build a branched
> oligosaccharide.
> > > There was some problem in the website I guess, because I was not able
> to
> > > download the pdb or prmtop files.
> >
> > You should take this up with the people who run the glycam site, which is
> > still by far the best option to create oligosaccharides. Of course,
> > provide
> > them with all the details you can.
> >
> > ....dac
> >
> >
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> >
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Mar 30 2017 - 06:00:02 PDT
