Dear Amber Users and Developers
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?
Also, Can the addions command in tleap be used to add the hydronium
ions inside the box?
Any suggestions would be greatly appreciated.
Sincerely,
Sam
--
*Samaneh ghassabi kondalaji*
*PhD student in Chemistry*
*555 CRL, Chemistry department*
*West Virginia University *
*Morgantown, USA*
*E-mail: **saghassabikondalaji.mix.wvu.edu*
<saghassabikondalaji.mix.wvu.edu>
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Received on Tue Apr 04 2017 - 19:00:05 PDT
