[gmx-users] non-glycosilated protein simulation

[Justin Lemkul]

On 5/23/15 9:16 AM, Homa rooz wrote:
> Can I remove ​carbohydrate part of glycosilated protein from pdb structure
> then run MD by gromos force field?
>

You *can* do anything, but the better question is if you *should* do that.  Is 
the carbohydrate important for function, stability, etc?  Are the dynamics of 
the nearby residues important to your study?

-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 629
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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