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Hi David,

With the version2 of GlcNH2_and_GlcNH3_0-4_link-v2.prep,  I cannot save prmtop files.

> glycan=sequence{OME 4Yn 4Yn 4Yn 4Yn 4Yn 0Yn}
> saveamberparm glycan chitosan.prmtop chitosan.inpcrd
Checking Unit.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Could not find angle parameter: Cg - Oh - Cg
Could not find angle parameter: Cg - Oh - Cg
Could not find angle parameter: Cg - Oh - Cg
Could not find angle parameter: Cg - Oh - Cg
Could not find angle parameter: Cg - Oh - Cg
Building proper torsion parameters.
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  Cg-Oh-Cg-H2
** No torsion terms for  Cg-Oh-Cg-Os
** No torsion terms for  Cg-Oh-Cg-Cg
** No torsion terms for  Cg-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  Cg-Oh-Cg-H2
** No torsion terms for  Cg-Oh-Cg-Os
** No torsion terms for  Cg-Oh-Cg-Cg
** No torsion terms for  Cg-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  Cg-Oh-Cg-H2
** No torsion terms for  Cg-Oh-Cg-Os
** No torsion terms for  Cg-Oh-Cg-Cg
** No torsion terms for  Cg-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  Cg-Oh-Cg-H2
** No torsion terms for  Cg-Oh-Cg-Os
** No torsion terms for  Cg-Oh-Cg-Cg
** No torsion terms for  Cg-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  H1-Cg-Oh-Cg
** No torsion terms for  Cg-Oh-Cg-H2
** No torsion terms for  Cg-Oh-Cg-Os
** No torsion terms for  Cg-Oh-Cg-Cg
** No torsion terms for  Cg-Cg-Oh-Cg

From: Users of GLYCAM & GLYCAM-Web [mailto:[log in to unmask]] On Behalf Of David Thieker
Sent: Tuesday, 7 March 2017 3:47 AM
To: [log in to unmask]
Subject: Re: GlcNH2

Hi Neha,
The beta linkage in the original and previously attached prep files was designated as 4YN. However, in order to match current Glycam nomenclature describing alpha/beta linkages, I have attached a modified version of the prep file where residue name 4YN refers to the alpha linkage. Therefore, when using GlcNH2_and_GlcNH3_0-4_link-v2.prep, change the tleap input file to use 4Yn in order to create a glycan with the beta linkage.
Best,
David

On Sun, Mar 5, 2017 at 6:43 PM, Neha S. Gandhi <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Thanks David.

Just to clarify, 4Yn is beta linkage?

Cheers,
Neha

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

quit
------------------------------------------------------------------------------------------
Please let me know if you have any other questions.

Best,
David



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