Dear all, I am adding Nitrogen box instead of water molecules to my protein. Based on your guidelines I generated the coordination and topology file of nitrogen. Then I used the following command: genbox -cp A_newbox -ci -42000mol N2C.gro -o A_solv.gro -p topol.top
N2C.gro is my new file made manually whithin all information in spc216.gro. I replaced all data in spc216.gro with N2C but I kept the name unchanged: genbox -cp A_newbox -ci -42000mol N2Cspc216.gro -o A_solv.gro -p topol.top The box was generated but there were 0 SOL molecules. The error is: Invalid command argument: spc216.gro How can I fix it? Thanks. Best regards, Sarah Keshavarz
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