Hey folks,
I’m blowing 25 year old cobwebs off of memories about generating Amber topology files when I wrote Leap’s topology file generator. I’m implementing a new one.
I wonder if core Amber developers could help me remember some things.
Non-bonded interactions are represented in the following way.
I’m using this for guidance (
http://ambermd.org/formats.html <
http://ambermd.org/formats.html>).
Atoms are represented by tables of properties (CHARGE, ATOMIC_NUMBER, AMASS, ATOM_TYPE_INDEX etc.).
Each atom_i has an entry in each of these tables at the same offset (i) from the start of each table.
Each atom_i has a list of excluded atoms that are excluded from non-bonded interaction calculations.
The NUMBER_EXCLUDED_ATOMS table lists for each atom(i) the number of other atoms that are excluded from non-bonded interactions with atom_i.
I’m going to use C-style indexing from 0 (zero) from here on.
The EXCLUDED_ATOMS_LIST contains these lists of excluded atoms for each atom_i. The list for atom_0 (first atom) starts at EXCLUDED_ATOMS_LIST(0) and goes for NUMBER_EXCLUDED_ATOMS(0)-1 entries.
The list for atom_1 starts at EXCLUDED_ATOMS_LIST(NUMBER_EXCLUDED_ATOMS(0)) and goes for NUMBER_EXCLUDED_ATOMS(1)-1.
From there I need to keep track of the sum of NUMBER_EXCLUDED_ATOMS(0) to NUMBER_EXCLUDED_ATOMS(i-1) to find the start of the excluded atoms list for atom_i.
QUESTION #1: The excluded atom lists are indices into the atom tables in increasing numerical order?
QUESTION #2: The excluded atom list only includes indices (j) where j>i for atom_i?
This is so that the non-bond calculation loop below can calculate the correct interactions:
for (atom_x = 0; atom_x<NATOM; ++atom_x) {
for (atom_y = atom_x+1; atom_y<NATOM; ++atom_y) {
if ( EXCLUDED_ATOMS_LIST(excluded_counter) == atom_y ) continue;
// calculate nonbonded interaction
}
}
QUESTION #3: Excluded atoms are 1-2 (stretch) and 1-3 (angle) interactions What about 1-4 (dihedral) interactions, are they in the EXCLUDED_ATOMS_LIST or not?
QUESTION #4: Is there anything important I’m missing about non-bonded interactions? Magical negative indices or values or something that have special meaning?
Please correct anything that I’m saying wrong above.
Christian Schafmeister
Professor, Chemistry Department
Temple University
meister.temple.edu <mailto:meister.temple.edu>
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Received on Wed Sep 21 2016 - 10:30:03 PDT
