Hi again, The genion doesn't work. I issue the following: $ genion -s fullmd.tpr -random -nname Cl -nn 8 -o out.gro -p test.top -g genion.log and get the error massage of: .... Processing topology ------------------------------------------------------- Program genion, VERSION 3.3.1 Source code file: futil.c, line: 340 File input/output error: test.top ------------------------------------------------------- If I don't use -p test.top in the command line, then it doesn't complain, but it stops after selecting the group and doesn't move forward. ... Group 11 ( Non-Protein) has 44823 elements Group 12 ( SOL) has 44823 elements Group 13 ( Other) has 44823 elements Select a group: 12 Selected 12: 'SOL' Number of (3-atomic) solvent molecules: 14941 Replacing solvent molecule 1752 (atom 6577) with Cl Any idea? Siavoush
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