Dear Amber Community,
In the BONDS_INC_HYDROGEN section of the topology file, each bond is identified by by 3 integers—the two atoms involved in the bond and the index into the BOND_FORCE_CONSTANT and BOND_EQUIL_VALUE.
My question is how is these integers for atoms assigned. I have a system of 1822 atoms, but the integers for identifying atoms in this section can go to 5400+, so apparently, they are not simply assigned according to the order of atoms. However, I could not figure out where is the mapping of those integers to the atoms. I wonder if somebody could kindly give me some explanation.
Sincerely,
Ge Song
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Received on Sun Jan 21 2024 - 20:30:02 PST
