[gmx-users] Option:Coupled to heme
jalemkul at vt.edu
Mon Mar 3 21:24:53 CET 2014
On 3/3/14, 2:23 PM, Gmail2 wrote:
> That is, option 3 is not deprotonated. Am I wrong?
Not fully deprotonated to the point of being anionic, no. Look at the .rtp
entry - it is identical to HISA.
> Then, how can I get deprotonated histidine?
Find a force field that has such a thing, or parametrize it yourself.
> Ahmet Yıldırım
> 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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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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