[gmx-users] Option:Coupled to heme

[Justin Lemkul]

On 3/3/14, 1:33 PM, Gmail2 wrote:
> Dear users,
>
> When I use the -his option of pdb2gmx for deprotonated the Histidine residue, I get the following options:
>   0. H on ND1 only (HISA)
>   1. H on NE2 only (HISB)
> 2. H on ND1 and NE2 (HISH)
> 3. Coupled to Heme (HIS1)
> Where option 3 is deprotonated. But it is named as a 'Coupled to heme'. Why option 3's name is not deprotonated HIS?
>

Because it's not.  HIS1 is just a delta-protonated histidine.  The different 
name (HIS1 vs. HISA) is required for specbond.dat to work properly.

-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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