AMBER Archive (2005)

Subject: Re: AMBER:how to deal with metal ion?

From: samuel.arey_at_epfl.ch
Date: Fri Dec 30 2005 - 05:05:39 CST

In Gaussian, use the option POP=(MK,READRADII)
and then put:

Ca 1.908

in the cards after the atomic coordinates. See the
online Gaussian help pages on POP.
(I think 1.908 Angstroms is the atomic radius of Ca
used by AMBER).

Sam

Quoting snowyowls <ethercui_at_gmail.com>:

> I using antechamber to deal with a ligand molecular
> there is a calcium ion in this molecular
> i want to using Gaussian to caculate it,useing the key word pop=MK
> but it failed because there is no radius for atom 34 atomic number
> 20
>
> i want to know how to deal with such kind of metal ion,
> can i change it into small atoms,such as Mg?
> or i should try some other programs?
>
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