VMD-L Mailing List

From: Georcki Ropon (groponp_at_gmail.com)
Date: Sat Nov 20 2021 - 13:35:42 CST

Hi Pietra,

For more complex neutralization you can use cionize , I use it for high charged systems (DNA, Ribosomes, etc,)

https://www.ks.uiuc.edu/Research/vmd/plugins/cionize/ <https://www.ks.uiuc.edu/Research/vmd/plugins/cionize/>

Best,

Geo.

> On Nov 20, 2021, at 10:11, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> Hello
> I am trying to carry out MD with a mono-positively charged organic molecule (small molecule, "natural product") in chloroform.
>
> It seems to me that there is no point - or no easy way - to neutralize. That mono-positively chrged molecule (NMR identified) represents one of the species in a complex environment containing the MsOH strong acid, and where the prevalent existing base is also an organic molecule
>
> thanks for advice
>
> francesco pietra