[gmx-users] Free oxygen in water AMBER FF definition to use in GROMACS

Ebert Maximilian m.ebert at umontreal.ca
Fri Oct 2 21:57:13 CEST 2015

I found a definition for oxygen in the paper: Effective Simulations of Gas Diffusion Through Kinetically Accessible Tunnels in Multisubunit Proteins: O2 Pathways and Escape Routes in T-state Deoxyhemoglobin 

they use CHARMM as FF and I will use AMBER99SB-ILDN so not ideal because it was not calculate with the same FF in mind but for such a simple molecule it should be fine.

have a good weekend,


> On Sep 24, 2015, at 5:59 PM, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
> Hi there,
> I wanted to know if anyone has AMBER FF definition of oxygen, which I could use to simulate oxygen in water. 
> Thank you very much,
> Max
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