I suspect a tutorial will describe how to set up an ion. Basically, the
coordinates can be 0, 0, 0; the atom type must be mapped to an element;
and R* and epsilon parameters must be provided for the atom type. Here
is an old paper that derives parameters for different ions in complex
with DNA:
Ion-Induced Stabilization of the G-DNA Quadruplex: Free Energy
Perturbation Studies. W.S. Ross and C.C. Hardin
Journal of the American Chemical Society 116, 6070 (1994).
Bill
On 2/16/16 9:06 PM, Sehrish Naz Aijaz wrote:
> Dear all,
> I am facing problem in performing MD simulation of a system enclosing ligand and mercury but I am unable to generate parameters for mercury metal ion as I did not have expertise in Gaussian (QM) and DFT. Can anyone provide me mercury parameter files because whenever I generate mercury.mol2 it shows zero XYZ coordinates with zero charge. I have tried nonbonded metal ion script for zinc ions but unable to generate parameter as my mercury.mol2 files is always blank with zero coordinates and charge. Please help me what should I do and if anyone can provide the parameter file for mercury. Thanks
>
> Regards,
>
> Sehrish Naz
> Jr. Research Fellow,
> Computational Chemistry Unit.
> Dr. Panjwani Center for Molecular Medicine and Drug Research,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75270.
>
>
> Sent from Mail for Windows 10
>
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Received on Tue Feb 16 2016 - 22:30:02 PST
