VMD-L Mailing List

From: Gumbart, JC (gumbart_at_physics.gatech.edu)
Date: Fri Apr 02 2021 - 15:43:20 CDT

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!qFM6Xy8WFEX5JtPAZVwzsmeCip7CHxI4Me9M1EE_S8spp4i74scITy0mYKnwMvynLg$

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<mailto:vermaasj_at_msu.edu>> wrote:

Hi Francesco,

Propka (https://urldefense.com/v3/__https://github.com/jensengroup/propka__;!!DZ3fjg!qFM6Xy8WFEX5JtPAZVwzsmeCip7CHxI4Me9M1EE_S8spp4i74scITy0mYKkmuRD4BA$ <https://urldefense.com/v3/__https://github.com/jensengroup/propka__;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFDRl_oZJA$>) or DelphiPka (https://urldefense.com/v3/__https://github.com/delphi001/DelphiPka__;!!DZ3fjg!qFM6Xy8WFEX5JtPAZVwzsmeCip7CHxI4Me9M1EE_S8spp4i74scITy0mYKmz4jPpAg$ <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<mailto:owner-vmd-l_at_ks.uiuc.edu>> on behalf of Francesco Pietra <chiendarret_at_gmail.com<mailto:chiendarret_at_gmail.com>>
Date: Friday, April 2, 2021 at 1:36 PM
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu>>, "henin_at_ibpc.fr<mailto:henin_at_ibpc.fr>" <henin_at_ibpc.fr<mailto:henin_at_ibpc.fr>>, "zhu13_at_llnl.gov<mailto:zhu13_at_llnl.gov>" <zhu13_at_llnl.gov<mailto: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<mailto: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<mailto: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