From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat Apr 03 2021 - 09:22:03 CDT

I tried propka: useless in my case. It runs also in the presence of genetic
material but it disregards it completely. HIS residues sheltered by
nucleosides are treated as surface HIS.

With https://urldefense.com/v3/__http://compbio.clemson.edu/sapp/delphi_webserver/__;!!DZ3fjg!oU_Y6aSXpWsMKMT-rIh1qm0lmoTZwWqeYwSUvavyHF528Gr8UUTbaV1Ji-_5CM9XnQ$ I was unable to load
a pdb file

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!oU_Y6aSXpWsMKMT-rIh1qm0lmoTZwWqeYwSUvavyHF528Gr8UUTbaV1Ji--0tAnLOQ$ ), 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!oU_Y6aSXpWsMKMT-rIh1qm0lmoTZwWqeYwSUvavyHF528Gr8UUTbaV1Ji-_a9nFdBQ$
> <https://urldefense.com/v3/__https:/pubs.rsc.org/en/content/articlelanding/2021/sc/d0sc04942e__;!!HXCxUKc!gvFYR3OpPr1fjuH1jJQ1NtrWmWfgzesHlw-bJ5W_WnlWlHNPuvfRXD9_XBJvm84$>
>
>
>
> We ran for 20 ns x 3, but you can often see a disruption sooner.
>
>
>
> Best,
>
> JC
>
>
>
> On Apr 2, 2021, at 2:26 PM, Vermaas, Josh <vermaasj_at_msu.edu> wrote:
>
>
>
> Hi Francesco,
>
>
>
> Propka (https://urldefense.com/v3/__https://github.com/jensengroup/propka__;!!DZ3fjg!oU_Y6aSXpWsMKMT-rIh1qm0lmoTZwWqeYwSUvavyHF528Gr8UUTbaV1Ji--0HkV2BA$
> <https://urldefense.com/v3/__https:/github.com/jensengroup/propka__;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFDRl_oZJA$>)
> or DelphiPka (https://urldefense.com/v3/__https://github.com/delphi001/DelphiPka__;!!DZ3fjg!oU_Y6aSXpWsMKMT-rIh1qm0lmoTZwWqeYwSUvavyHF528Gr8UUTbaV1Ji-8k_6AmHQ$
> <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
>
>
>