Hand editing of the PSF should not be necessary. Note that for regenerating the PSF you do not need to perform any coordinate manipulations, all you need to know is how many molecules you have of a certain type, not where they are. Let's say you start with 100 water molecules, then add 30 solute molecules and delete 50 water molecules. To regenerate this PSF you can either
read seque tip3 50
gene wat noangle nodihe
read seque myml 30
gene solu

Sequences could also be read from coordinate files (one for each segment) prepared from the final state of your inital setup.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden