[gmx-users] protonation of histidines

[Justin Lemkul]

On 6/2/16 2:04 PM, Irem Altan wrote:
> Hi,
>
> Thanks. Is there something I can read to get more information as to how this is done?
>

The source code.

It's just a hydrogen bond search.  If the putative donor and acceptor atoms 
satisfy the typical distance cutoff (0.35 nm) and angle (>= 150) then it's a 
hydrogen bond and the histidine residue is protonated accordingly.

-Justin

> Best,
> Irem
>
>> On Jun 2, 2016, at 1:06 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>>
>> Hi Irem,
>>
>> pdb2gmx checks the hydrogen bonding network and decides which form of His
>> fits best.
>>
>> Cheers,
>>
>> Tsjerk
>> On Jun 2, 2016 17:20, "Irem Altan" <irem.altan at duke.edu> wrote:
>>
>>> Hi,
>>>
>>> When I process a .pdb structure using pdb2gmx, how does Gromacs add
>>> hydrogens to the histidine residues? I see that in the processed structure,
>>> some histidines have their NE2 atom protonated, while some have ND1
>>> protonated. How does Gromacs decide which nitrogen to protonate?
>>>
>>> Best,
>>> Irem
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=NeKtPfZmomO7TY28nP-DKDvbsgZ5lLg68UpgcmP1B_Y&e=  before
>>> posting!
>>>
>>> * Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=1re0r4wCl8tw_YjRBOs7agHtwsReTnobB68U_GgXnf4&e=
>>>
>>> * For (un)subscribe requests visit
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=s1JlpSKFO9QEGwEr2Ud8DphQ33LwK9vu_EXIy8iv3Ao&e=  or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists_GMX-2DUsers-5FList&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=NeKtPfZmomO7TY28nP-DKDvbsgZ5lLg68UpgcmP1B_Y&e=  before posting!
>>
>> * Can't post? Read https://urldefense.proofpoint.com/v2/url?u=http-3A__www.gromacs.org_Support_Mailing-5FLists&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=1re0r4wCl8tw_YjRBOs7agHtwsReTnobB68U_GgXnf4&e=
>>
>> * For (un)subscribe requests visit
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__maillist.sys.kth.se_mailman_listinfo_gromacs.org-5Fgmx-2Dusers&d=CwICAg&c=imBPVzF25OnBgGmVOlcsiEgHoG1i6YHLR0Sj_gZ4adc&r=r1Wl_e-3DAvYeqhtCRi2Mbok8HBpo_RH4ll0E7Hffr4&m=PheuSeiRLbDQ1jCYrKCsKyLU_ZCIQHxVwZawG5XASew&s=s1JlpSKFO9QEGwEr2Ud8DphQ33LwK9vu_EXIy8iv3Ao&e=  or send a mail to gmx-users-request at gromacs.org.
>

-- 
==================================================

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

==================================================