VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Apr 02 2021 - 11:52:43 CDT

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