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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