[gmx-users] zero SOL molecules

sarah k dailycolors at gmail.com
Sun Mar 6 13:08:45 CET 2011

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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