[gmx-users] Question about n-linked glycans

[Justin Lemkul]

On 9/27/14 11:15 PM, Mikhail Yustanov wrote:
> Hi all,
>
> I am trying to study the influences of N linked glycans on protein stability. I am very new to MD Simulations. I wonder what is the best way to generate a topology file for the glycoprotein. Is there AMBER/GLYCAM integrated force field presently available? I have read through the basic and membrane tutorial but am still lost.
>

I don't know whether there are force field files available, but I know plenty of 
people have posted GLYCAM questions to the list, so presumably there are.

The biggest issue you'll have is the branched nature of these compounds. 
Getting a sugar attached to an amino acid will require modification of 
specbond.dat to create the non-linear bonds.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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