AMBER Archive (2006)

Subject: Re: AMBER: question about the topology file

From: Carlos Simmerling (carlos_at_csb.sunysb.edu)
Date: Wed Nov 08 2006 - 06:18:58 CST

the excluded atom list will containt atoms with higher number
that are 1-1, 1-2, 1-3 and 1-4 to this atom. yes, that can be quite
a few atoms, including all atoms in the same ala residue for the N.

J. Zhang wrote:

>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 amber_at_scripps.edu
>To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu