AMBER Archive (2009)

Subject: Re: [AMBER] zeros in excluded atom list in topology file

From: case (
Date: Fri Nov 06 2009 - 16:44:04 CST

On Thu, Nov 05, 2009, Peter Schmidtke wrote:
> I wondered why there were zeros in the excluded atom list in the amber
> topology (parm) file of my system. I run simulations with explicit solvent
> and for example each water molecule has 2 (O), 1 (H), 1 (H) excluded atoms
> for calculating the non bonded interactions. But the single excluded atom
> for the second H atom points to atom 0 which does not exist, why?

Amber indeed has a rather weird data structure for storing the exclusion list:
an atom with no excluded atoms is represented as having one excluded atom
with label "0". Reasons for this are shrouded in pre-history, but we have
maintained backward compatibility to prmtop files that were written long, long
ago. Although the data structure in the file is odd, I think the actual data
strutures constructed in memory are rather more logical.


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