How to edit .psf file? (remove unwanted atoms)

How to remove atoms from the psf file?

Assume that you have the .psf file of the whole system (e.g. RNA, waters and ions) and you want to  remove water molecules from .psf file. You can edit the psf file it in the VMD program.

First open the TkConsole. Than select atoms you want save in new psf:
> set rna [atomselect top „all not water”]
rna is the variable name that you will use for the selection.
Next write new .psf:
> $rna writepsf rnarna-nowat.psf

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