Hi Ana,

I've attached GlcNH3_alpha-beta.prep, which includes the alpha (3YP 4YP WYP 0YP) and beta (3Yp 4Yp WYp 0Yp) GlcNH3+ residues. The following is an example tleap input script for building a beta 1-4 oligomer:

#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/GlcNH3_alpha-beta.prep

# Create the glycan sequence, note that the sequence begins from the reducing end of the glycan
glycan = sequence { OME 4Yp 4Yp 4Yp 0Yp }

saveamberparm glycan molecule.prmtop molecule.rst7
savePDB glycan molecule.pdb


Please let me know if you have any other questions.


*Note these prep files were derived from 0YNP and 0YnP within GlcNH2_and_GlcNH3.prep

On Wed, Mar 29, 2017 at 5:47 AM, Ana Poveda <[log in to unmask]> wrote:
Hi David,

In your prep file GlcNH2_and_GlcNH3_0-4_link-v2.prep there are only GlcNH2 residues with open valence at the 4 position. how can I build a GlcNH3 beta 14 oligomer?



David F. Thieker
PhD Candidate
Biochemistry and Molecular Biology
Complex Carbohydrate Research Center
University of Georgia, Athens, GA