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Thanks for your time Lachele.

On Mon, Nov 23, 2015 at 1:39 AM, Lachele Foley <[log in to unmask]> wrote:

> They are on the way.  The student who developed them successfully
> defended her thesis (Yay!) just recently.  For that reason and several
> others, you've caught us when we are a bit over-stressed.  The
> information should be available very soon.  We will announce it here
> and on the AMBER reflector.
>
>
> On Sun, Nov 22, 2015 at 10:17 AM, anu chandra <[log in to unmask]> wrote:
> > Hello Lachele,
> >
> > Thanks for prompt reply. I do understand the limitation of current naming
> > convention in Glycam. It will be grateful, as you mention, if you can
> > provide the prep file in 'Special release' section for 4DGlcpNSa1, which
> I
> > can successively use for the heparin
> > (LIdopA[2S]a1-4DGlcpNS[6S]a1-4LIdopA[2S]a1-4DGlcpNS[6S]a1-OH) I build on
> > GAG-Builder.
> >
> >
> > Many thanks
> > Anu
> >
> > On Fri, Nov 20, 2015 at 6:10 AM, Lachele Foley <[log in to unmask]>
> wrote:
> >>
> >> It is correct for there to be no residue RYA in GLYCAM_06j-1.prep.  To
> >> use the name RYA makes logical sense, so I understand why it was
> >> chosen, but it technically isn't the correct name to use.
> >>
> >> The current GLYCAM residue naming convention has numerous limitations,
> >> and you have just encountered one.  A new naming convention was
> >> proposed in the article at the link just below.  We want to switch to
> >> this, or some other, more flexible naming convention, but doing so
> >> will not be a trivial task and must be done with great care and
> >> attention to detail.
> >> http://glycob.oxfordjournals.org/content/18/6/426.full.pdf+html
> >> (proposed new naming)
> >>
> >> So, Anu, I understand that your choice of the name RYA signifies the
> >> fact that an SO3 is attached at positions 2 and 6, with another
> >> monosaccharide at position 4.  However, our naming doesn't recognize
> >> an 'N' as an attachment position in that sense.  The naming, at least
> >> thus far, has only considered open valences at hydroxyl oxygens.  So
> >> there is no definition at all for attachments at "position 2" of a
> >> GlcNAc or similar residue - note that there is also no residue called
> >> '2YA' in the prep file.
> >>
> >> BTW, the RYA in Table 4 on our naming page (glycam.org/naming) is a
> >> typo that has been present, but not noticed, since around the release
> >> of GLYCAM-04.
> >>
> >> To other Woods/GLYCAM folks... We *could* adopt this naming, allowing
> >> N to be an open valence.  So, 2YA would be -2DGlcpNa1- with an open
> >> valence at the N, which is at the 2 position.  That might simplify
> >> things in the meantime.  We might not be able to generate all the
> >> NAc-relevant residues in the database, but there would be names for
> >> many of them.  Also, this still doesn't give us a plain GlcpN, but we
> >> don't have that anyway.  It also might allow things to be attached
> >> there that should not be.  We could check to see if a lack of ff
> >> parameters would keep this from being a problem in a simulation.
> >>
> >> Back to everyone:  In the background, the builder currently calls the
> >> files xYS for alpha and xYs for beta (for a lack of an official naming
> >> convention).  So, 4YS is -4DGlcpNSa1- and so forth.  I can post those
> >> prep files for now in the "Special Releases" section.  I think that is
> >> all Anu needs.  We can always update the names and such later as
> >> desired.
> >>
> >>
> >> --
> >> :-) Lachele
> >> Lachele Foley
> >> CCRC/UGA
> >> Athens, GA USA
> >
> >
>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>