Dear Amber Developer,
I'm just trying to ignore specific non-bonded interactions,
e.g. a set of atoms in protein vs an ion molecules.
To achieve the purpose,
I modify "%FLAG NUMBER_EXCLUDED_ATOMS" and "%FLAG EXCLUDED_ATOMS_LIST"
in PRMTOP file but It does not work at all, thus giving same energy.
I'd like to know how I can make a specific non-bond interaction off.
Yours sincerely,
Ikuo KURISAKI
PS
Let's assume that I make off protein-ion interaction.
When I tried t modify a PRMTOP file,
I added the ion's atom number to components of excluded atom list
associated with protein.
Components of number excluded atoms were also modified
Corresponding to the above modification.
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Received on Mon Jun 10 2013 - 03:30:02 PDT
