[gmx-users] Regarding Glycine structure

[Justin Lemkul]

On 3/23/17 2:05 PM, Dilip H N wrote:
> Hello,
>
> I have a non zwitter ionic glycine molecule [NH2CH2COOH] in water, and in
> the first step if i do the energy minimization and then visualizes the
> mixture, the glycine is no more in its pure form as before instead it has
> been converted to its zwitter ionic form [NH3CH2COO], and some Hydrogen
> bonds with water are also broken. How can i solve these both issues..??
>

Glycine didn't convert between forms.  That's impossible; bonds can't break or 
form in a molecular mechanical process.  The termini are exactly what you 
assigned them to be.  If you want them to be something else, you have to assign 
them as such with pdb2gmx.  Though you should note that NH2 and COOH can't 
coincide at any real pH value.

-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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