From: Miro Astore (miro.astore_at_gmail.com)
Date: Sat Apr 03 2021 - 19:28:57 CDT

You might consider constant ph simulations? They're supported in namd.

On Sat., 3 Apr. 2021, 6:43 pm Francesco Pietra, <chiendarret_at_gmail.com>
wrote:

> Hi Josh and James
> I had already seen another checking the MD stability for the various
> protonation states of HIS:
>
> Histidine protonation and the activation of viral fusion proteins, Daniela
> S. Mueller, Thorsten Kampmann, Ragothaman Yennamalli, Paul R. Young,
> Bostjan Kobe
> and Alan E. Mark, Biochemical Society Transactions (2008) Volume 36, part 1
>
> With so many HISs as in my case, the combinations scale tremendously up
> and one fears to miss the most important overall state.
> There is a need of new software to assign the protonation states of HIS.
> Also, if there is a fine tuning of HSE vs HSD, changeable during MD in
> response to the interaction with the strongly negative electrostatics of
> the nucleosides, things become complicated indeed.
>
> But I'll read James' paper and I'll try the suggested Propka and
> DelphiPKa, if not else to see the output.
>
> What about the famous ROSETTA? Perhaps, however, it just uses Propka or
> Delphi PKa.
>
> thanks
> francesco
>
> On Sat, Apr 3, 2021 at 1:35 AM Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>
>> Admittedly, it has been a while since I looked at propka output in
>> detail, but when I run regular proteins through pdb2pqr (
>> https://urldefense.com/v3/__https://server.poissonboltzmann.org/__;!!DZ3fjg!tcs8H7CAwISj1RPL31O1aqHPfXRn2hVik8b8Snrcrgi3pcAYxmICWImmNxQeDOYaTQ$
>> <https://urldefense.com/v3/__https://server.poissonboltzmann.org/__;!!DZ3fjg!tsqIFHVKijNxX_B1fbFz9jygI2pMsbnGZC8el-7pPOZ9fT3WcvW5y8s__expakzqDA$>),
>> it claims to use PropKa to assign charges, and the pqr files that come out
>> definitely seem to have a made an attempt to choose between HSD and HSE, so
>> I assume there is something in the PropKa output that it is using to
>> determine histidine protonation. For the applications I was using it for,
>> this level of detail has been fine, but JC is right, you can also just try
>> all protonation state combinations and see what makes sense.
>>
>>
>>
>> -Josh
>>
>>
>>
>> *From: *"Gumbart, JC" <gumbart_at_physics.gatech.edu>
>> *Date: *Friday, April 2, 2021 at 4:43 PM
>> *To: *"Vermaas, Josh" <vermaasj_at_msu.edu>
>> *Cc: *Francesco Pietra <chiendarret_at_gmail.com>, VMD Mailing List <
>> vmd-l_at_ks.uiuc.edu>, "henin_at_ibpc.fr" <henin_at_ibpc.fr>, "zhu13_at_llnl.gov" <
>> zhu13_at_llnl.gov>
>> *Subject: *Re: vmd-l: histidine protonation
>>
>>
>>
>> I’m not sure about DelphiPka, but Propka doesn’t tell you which nitrogen
>> to put the proton on. We found running simulations of different states and
>> checking their stability to be the most reliable (albeit more
>> time-consuming) way to assign protons to histidines:
>> https://urldefense.com/v3/__https://pubs.rsc.org/en/content/articlelanding/2021/sc/d0sc04942e__;!!DZ3fjg!tcs8H7CAwISj1RPL31O1aqHPfXRn2hVik8b8Snrcrgi3pcAYxmICWImmNxSaO7Fc4A$
>> <https://urldefense.com/v3/__https:/pubs.rsc.org/en/content/articlelanding/2021/sc/d0sc04942e__;!!HXCxUKc!gvFYR3OpPr1fjuH1jJQ1NtrWmWfgzesHlw-bJ5W_WnlWlHNPuvfRXD9_XBJvm84$>
>>
>>
>>
>> We ran for 20 ns x 3, but you can often see a disruption sooner.
>>
>>
>>
>> Best,
>>
>> JC
>>
>>
>>
>> On Apr 2, 2021, at 2:26 PM, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>>
>>
>>
>> Hi Francesco,
>>
>>
>>
>> Propka (https://urldefense.com/v3/__https://github.com/jensengroup/propka__;!!DZ3fjg!tcs8H7CAwISj1RPL31O1aqHPfXRn2hVik8b8Snrcrgi3pcAYxmICWImmNxQydtb_0w$
>> <https://urldefense.com/v3/__https:/github.com/jensengroup/propka__;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFDRl_oZJA$>)
>> or DelphiPka (https://urldefense.com/v3/__https://github.com/delphi001/DelphiPka__;!!DZ3fjg!tcs8H7CAwISj1RPL31O1aqHPfXRn2hVik8b8Snrcrgi3pcAYxmICWImmNxQ4a3AsCw$
>> <https://urldefense.com/v3/__https:/github.com/delphi001/DelphiPka__;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFCAQcr_zA$>)
>> in principle should be able to handle non-protein ionizable groups.
>>
>>
>>
>> -Josh
>>
>>
>>
>> *From: *<owner-vmd-l_at_ks.uiuc.edu> on behalf of Francesco Pietra <
>> chiendarret_at_gmail.com>
>> *Date: *Friday, April 2, 2021 at 1:36 PM
>> *To: *VMD Mailing List <vmd-l_at_ks.uiuc.edu>, "henin_at_ibpc.fr" <
>> henin_at_ibpc.fr>, "zhu13_at_llnl.gov" <zhu13_at_llnl.gov>
>> *Subject: *vmd-l: histidine protonation
>>
>>
>>
>> Hi
>>
>> I am faced with the problem of establishing the protonation status of
>> many histidine residues present in a nucleic acid-protein ensemble, both
>> inside and on the periphery. All that in the framework of CHARMM36 for NAMD
>> MD.
>>
>>
>>
>> Servers for direct assignment, like H++, are useless because of the
>> presence of nucleic acids.
>>
>>
>>
>> I came across two interesting old posts by Zhu and Henin to this concern
>> and wonder whether there is anything additionally useful for the above
>> ensemble
>>
>> *From:* Fangqiang Zhu (*fzhu_at_ks.uiuc.edu*
>> <fzhu_at_ks.uiuc.edu?Subject=Re:%20%20how%20can%20I%20know%20which%20type%20HIS%20belong%20to?(HSD,HSE,HSP)>
>> )
>> *Date:* Sat Nov 29 2003 - 00:22:03 CST
>>
>> *From:* Jérôme Hénin (*jerome.henin_at_uhp-nancy.fr*
>> <jerome.henin_at_uhp-nancy.fr?Subject=Re:%20%20how%20can%20I%20know%20which%20type%20HIS%20belong%20to?(HSD,HSE,HSP)>
>> )
>> *Date:* Sat Nov 29 2003 - 04:37:30 CST
>>
>> Thanks for advice
>>
>> francesco pietra
>>
>>
>>
>