Actually... the docs are probably right, and the prep file is
misnamed.  I think N was supposed to be alpha.  This follows 0GL
(Neu5Gc) being alpha and some others like tyvelose, where 0TV is alpha
and 0Tv is beta.



On Fri, Mar 3, 2017 at 6:02 PM, David Thieker <[log in to unmask]> wrote:
> Hi Neha,
>
> The prep files that were available did not include an open valence at the 4-position. I've adapted those prep files to create the 4-linked parameters (attached).
>
> I noticed that the documentation incorrectly describes the linkage orientations for the glucosamine residues. The 4YN residue refers to the beta-linkage, whereas the 4Yn residue is alpha.
>
> The following is an example tleap script that builds a repeating unit of beta-GlcNH2:
>
> ------------------------------------------------------------------------------------------
> #tleap input file
> set default PBradii mbondi2
> source leaprc.GLYCAM_06j-1
> # Change the path for the prep to match the location on your system:
> loadamberprep /home/david/prep_files/GlcNH2_and_GlcNH3_0-4_link.prep
>
> # The file that I have attached connects to the O6 atom by default - this can be corrected by explicitly designating the O4 atom (this is a bug for 4YN, but 4Yn does not require the following line).
> set 4YN tail 4YN.1.O4
> # Create the glycan sequence, note that the sequence begins from the reducing end of the glycan
> glycan = sequence { OME 4YN 4YN 4YN 4YN 4YN 4YN 4YN 0YN }
>
> saveamberparm glycan chitosan.prmtop chitosan.rst7
> savePDB glycan chitosan.pdb
>
> quit
> ------------------------------------------------------------------------------------------
> Please let me know if you have any other questions.
>
> Best,
> David



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA