AMBER Archive (2009)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Nov 05 2009 - 18:39:56 CST

sorry if this is obvious, but are you sure you know how to read the
exclusion list? it's a pointer for each atom, not an actual list.

On Thu, Nov 5, 2009 at 12:06 PM, Peter Schmidtke
<pschmidtke_at_mmb.pcb.ub.es>wrote:

> Dear Amber Mailing list readers,
>
> 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?
>
> I saw also some zeros within the protein...why? Is this some amber internal
> coding saying that we have to do something special with this H atom, like a
> 10-12 potential instead of the 6-12? If yes, what is done in the Coulomb
> potential then?
>
> Thanks in advance for your reply.
>
> Best regards.
>
> --
>
> Peter Schmidtke
>
> ----------------------
> PhD Student at the Molecular Modeling and Bioinformatics Group
> Dep. Physical Chemistry
> Faculty of Pharmacy
> University of Barcelona
>
>
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