[gmx-users] Option:Coupled to heme

[Gmail2]

That is, option 3 is not deprotonated. Am I wrong? 
Then, how can I get deprotonated histidine?

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
> 
> -- 
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
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> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
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