Thank you, David!


On Mon, Mar 6, 2017 at 12:47 PM, David Thieker <[log in to unmask]> wrote:
> 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
>
>



-- 
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA