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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]] *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]] 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