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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Received on Wed Mar 29 2017 - 06:00:06 PDT
