From: Vermaas, Josh (
Date: Fri Apr 02 2021 - 13:26:13 CDT

Hi Francesco,

Propka (;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFDRl_oZJA$ ) or DelphiPka (;!!DZ3fjg!qLqvG5aUIsZadcvLdv2KKVS99Ta3HEX53KL7IdL8pM3CNQJ6bPm9CzlpqFCAQcr_zA$ ) in principle should be able to handle non-protein ionizable groups.


From: <> on behalf of Francesco Pietra <>
Date: Friday, April 2, 2021 at 1:36 PM
To: VMD Mailing List <>, "" <>, "" <>
Subject: vmd-l: histidine protonation

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 (<,HSE,HSP)>)
Date: Sat Nov 29 2003 - 00:22:03 CST
From: Jérôme Hénin (<,HSE,HSP)>)
Date: Sat Nov 29 2003 - 04:37:30 CST
Thanks for advice
francesco pietra