Hi,
I think this should just work if you specify a second mask (the
"solvent" mask) selecting your lipid headgroups:
watershell <solute mask> <lipid headgroup mask>
You may need to play around with the exact cutoffs ('lower' and
'upper'); the defaults (3.4 and 5.0 Ang respectively) assume you're
dealing with water.
Hope this helps,
-Dan
On Mon, Mar 7, 2022 at 6:57 AM Vic De Roo <Vic.DeRoo.ugent.be> wrote:
>
> Dear all,
> I am looking if there exists anything like “watershell” but instead of selecting the WAT molecules, it selects other specified atoms. In essence, I would like to know throughout the trajectory how many lipid headgroups (PC) are in the near vicinity of my solute. I guess this should be possible.
>
> Could anyone provide me with the exact command in that sense? This would be highly appreciated.
>
> Vic De Roo
> PhD Student
> NMRSTR Group<https://www.ugent.be/we/orgchem/nmr-structure-analysis/en>
> Department of Organic and Macromolecular Chemistry
> Krijgslaan 281, S4-bis, 1st floor
> B-9000 GENT
> Belgium
> +32456123894
>
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Received on Mon Mar 07 2022 - 08:30:02 PST
