What do you mean the "AMBER parameters for water" ?
The parameters in the usual parm9x Cornell et al.
force fields are TIP3P.
jim
On Mon, 18 Jun 2001, Satyavani Vemparala wrote:
>
> Hi,
> while simulating water, i used the parameters from the TIP3 model(
> ref:Jorgensen et al. J.chem.Phys vol.79,1983). I had no problem. But since
> i have an interest in simulating biological systems in water, i used the
> AMBER parameters for water, but had some pathological problems. The LJ
> repulsion parameters between oxygen-oxygen 'seems' to be unable to counter
> the huge attraction between hydrogen and oxygen( of two different water
> molecules). Why is that so?.. i other words why were the parameters for
> the Lennard-Jones potential changed in AMBER?
>
> Can i use TIP3 water parameters and for protiens AMBER parameters? or..is
> it essential to use AMBER parameters for both proteins and water?
>
> Thanks
> vani
>
>
>
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Received on Tue Jun 19 2001 - 11:52:04 PDT
