AMBER Archive (2009)

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

From: Peter Schmidtke (
Date: Fri Nov 06 2009 - 18:07:44 CST

On Fri, 6 Nov 2009 17:44:04 -0500, case <> wrote:
> 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
>> 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
> 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.
> ...dac

Thank you David for the clear answer!


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Peter Schmidtke

---------------------- PhD Student at the Molecular Modeling and Bioinformatics Group Dep. Physical Chemistry Faculty of Pharmacy University of Barcelona

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