Hi Neha,

You're almost there. Just set the tail of the residue to be the 4-position. The following works for me:

set 4Yn tail 4Yn.1.O4
glycan = sequence { OME 4Yn 4Yn 4Yn 4Yn 4Yn 4Yn 4Yn 0Yn }
saveamberparm glycan chitosan.prmtop chitosan.rst7
savePDB glycan chitosan.pdb

Best,
David

On Tue, Mar 14, 2017 at 8:14 PM, Neha S. Gandhi <[log in to unmask]> wrote:

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]EDU] 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]> 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]EDU] 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

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

 




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