AMBER Archive (2006)

Subject: AMBER: question about the topology file

From: J. Zhang (
Date: Wed Nov 08 2006 - 03:24:10 CST

Dear AMBER users,

I have a question about the excluding list in the %FLAG EXCLUDED_ATOMS_LIST
section in the topology file.

By reading the egb.f, I knew that the excluding list is to exclude pairs when
calculating the LJ and electrostatics terms. Now my question is, whether this
list is used by sander in calculations with explicit water and non-LES simulations?

I also take a look at the excluding list, and find something strange. For example,
for the first N atom in the residue NALA (the first residue in my protein),
the corresponding number of excluded atoms is 12, including all the other atoms
in the first residue NALA, as well as the first N atom in the second residue.
WHY so many atoms are excluded?

I can not track the program to find the answer by myself, since the excluded list
is stored in ix() array, which stores so many different kinds of information,
making the program is difficult to track.

Thank you very much for your help!

J. Zhang, Dr.

Institute of Biophysics
Nanjing University

----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to