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From: Raman Preet Singh (ramanpreetsingh_at_hotmail.com)
Date: Fri Aug 16 2024 - 09:05:20 CDT

Hi All,

I have created a coordinates file of a spherical nanoparticle and want to modify the surface groups. For this, I need the index of atoms on surface. I tried using the surface command as: surface top 1 2.5 2.5. However, the Tk console gave an error message: invalid command name "surface".

Another approach I tried was
set sel [atomselect top all]
surface $sel 1 2.5 2.5
This also gave the error message: invalid command name "surface"

I also tried selecting atoms using equation of sphere (x^2 + y^2 + z ^2 > r^2) but this too was
An alternative method I could think of is to identify atoms within a certain cutoff from solvent. Since the topology of nanoparticle is not yet ready, the equilibration steps with solvent could not be performed thus I dropped this approach.

Can anyone please guide through this.

Thanks,
Raman