The topology file you posted has a completely different count. Are you presenting the number of atoms in each molecule type in the list above? I’m sorry, but I won’t go through all your molecule types to find out how many atoms there are in each. I don’t mean to be unhelpful, but I’m sure you can find ways to count the number of molecules you’ve got of each type in your gro file and update the topology file yourself. If you can’t think of anything else then:
- Start with the first molecule type in your coordinate file (7wc4) count the number of atoms of that molecule type (i.e., scroll until you find the next molecule type).
- Check the number of atoms in the corresponding itp file (or in the topology file itself if it’s written there).
- Divide the number you counted in 1 by the number you counted in 2. For 7wc4 I expect you get 1 molecule.
- Make sure that the number you got in 3 matches the number of the corresponding molecule type (in the order they are listed) in the topology file.
- Redo from 1 with the next molecule type in your coordinate file.
Keep in mind that all molecules of the same type do not necessarily follow each other. E.g., have a look at POPC in your topology file. I’m not saying this is the quickest way to do it, but it will always work, or you are doing something wrong.