On Tue, Apr 04, 2017, Samaneh Ghassabi Kondalaji wrote:
> I am attempting to perform a simulation that requires Baaden hydronium
> ions in a tip3p water box as provided here:
> http://research.bmh.manchester.ac.uk/bryce/amber
> Using the frcmod, pdb as well as the prep files provided, the atom type
> definitions as H, OW and HW eventually leads to generation of a prmtop
> file where the atom type definitions for both H3O+ ions and tip3p water
> molecules are the same (OW AND HW) although the charge values are
> distinguished. I was trying to modify the initial force field files for H3O
> by replacing H and HW with H3, but I couldn't find any replacement for
> OW that matches the amber atom type. Is there any particular atom type that
> can be used to represent the Amber atom type for the O atom in hydronium
> ion?
You probably want to make up your own atom type: choose a two-letter type
that is not otherwise being used, and assign the hydronium ion parameters
to it. (Do the same thing for hydrogen: don't try to re-use an existing
atom type.)
> Also, Can the addions command in tleap be used to add the hydronium
> ions inside the box?
Yes. (As far as I know--haven't tried it. AddToBox is another common way
to add waters and ions around a solute.)
...dac
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Received on Wed Apr 05 2017 - 05:00:03 PDT
