[gmx-users] Option:Coupled to heme
ahmedo047 at gmail.com
Mon Mar 3 20:23:58 CET 2014
That is, option 3 is not deprotonated. Am I wrong?
Then, how can I get deprotonated histidine?
3 Mar 2014 tarihinde 20:43 saatinde, Justin Lemkul <jalemkul at vt.edu> şunları yazdı:
>> 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 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
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