[gmx-users] making topology file manually

[Mohsen Ramezanpour]

Dear All,

I am trying to insert a 5-atom ring composed of carbon and non-carbon atoms
in the middle of my small molecule.

Reading literature, I have got confused a bit. Especially about the
"pairs", "exclusions", and "improper dihedrals" sections in topology file.

Is anyone aware of any step-by-step tutorial for manually making a topology
file for a small molecule from scratch, or modifying it manually? I
appreciate it in advance for letting me know.

Best,
Mohsen






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