Dear Lachele,
Thankyou for the reply, I explicitly issued "bond" commands to re-link the
branches in tleap and it is working fine.
Regards
Manju
On Thu, Mar 30, 2017 at 6:09 PM, Lachele Foley <lf.list.gmail.com> wrote:
> 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 Sat Apr 01 2017 - 03:30:02 PDT
