Thanks David.

Just to clarify, 4Yn is beta linkage?


-----Original Message-----
From: Users of GLYCAM & GLYCAM-Web [mailto:[log in to unmask]] On Behalf Of David Thieker
Sent: Saturday, 4 March 2017 9:02 AM
To: [log in to unmask]
Subject: Re: GlcNH2

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

Please let me know if you have any other questions.