AMBER Archive (2009)

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

From: Peter Schmidtke (
Date: Thu Nov 05 2009 - 11:06:41 CST

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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