VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Apr 15 2021 - 09:35:08 CDT

Hi all
I went through, observing that Josh is correct: propka 3.4.0 (or 3 in
general) does tell you where the protons are, better so when the propka
output is coupled to a graphical examination. Whether the assignments can
be correct when other stuff is present, as in my case, is another matter,
although the other matter is felt. Unfortunately, it seems that the propka
inventors are no more involved in developing their software, so that the
question remains unresolved.

DelphipKa uses propka. And propka 3 is used by commercial software
companies. Whether as it is ,or by developing it, I don't know. H++ gets
stuck when other matter is present.

Hope that this saves time to op. Should anyone know the matter better......

francesco

On Fri, Apr 2, 2021 at 10:43 PM Gumbart, JC <gumbart_at_physics.gatech.edu>
wrote:

> 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!qKqwZJ5e3BsOIfV526wRDlQL2DH9Rjmz7Y4HH53AqvFWhc_lw3qq2Za972hvhIf6uA$
>
> 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!qKqwZJ5e3BsOIfV526wRDlQL2DH9Rjmz7Y4HH53AqvFWhc_lw3qq2Za972hnsNu_qg$
> <https://urldefense.com/v3/__https://github.com/jensengroup/propka__;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFDRl_oZJA$>)
> or DelphiPka (https://urldefense.com/v3/__https://github.com/delphi001/DelphiPka__;!!DZ3fjg!qKqwZJ5e3BsOIfV526wRDlQL2DH9Rjmz7Y4HH53AqvFWhc_lw3qq2Za972hNl7vxbw$
> <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
>
>
>