Re: [AMBER] Atom Index in the BONDS_INC_HYDROGEN Section of Topology

From: He, Amy via AMBER <amber.ambermd.org>
Date: Mon, 22 Jan 2024 04:30:39 +0000

Hi,

Check out the description of the BONDS_INC_HYDROGEN section at: https://ambermd.org/FileFormats.php
And see if the following rule applies:
NOTE: the atom numbers in the following arrays that describe bonds, angles, and dihedrals are coordinate array indexes for runtime speed. The true atom number equals the absolute value of the number divided by three, plus one.

--
Amy He
Hadad Lab . OSU
He.1768.osu.edu
From: Ge Song via AMBER <amber.ambermd.org>
Date: Sunday, January 21, 2024 at 11:21 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: [AMBER] Atom Index in the BONDS_INC_HYDROGEN Section of Topology
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 - 21:00:02 PST