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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 >