Hi,
I was very excited to discover Gromacs and decided to learn by following a few tutorials I found online. However, I ran into a problem: After filling up the simulation box with SPC water using genbox, the program backed up the topology file into another file with its name flanked by #, and left me with an empty topology file. Without knowing what had happened I went ahead and ran grompp, which exited with a fatal error, saying the number of atoms in the topology file does not match that of the coordinate file. I tried to use the backed up topology file, or to generate a new topology file using pdb2gmx, but ended up with the same error message. Grompp thinks there is no atom in the topology files. Does anyone know what is going on? Also, water molecules don't seem to appear in topology files. Does that matter? Thank you very much if you have read this much. Any idea what's going on. Your help will be greatly appreciated. Yun Li Assistant Professor of Chemistry Delaware Valley College 700 E. Butler Ave., Doylestown, PA 18901 (215) 489-2482
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