Hi Tom,
It depends on which model you are going to use: the bonded model (you may need to use the restrained nonbonded model if you have two water molecules coordinating to the same ferrous ion), or the nonbonded model.
There is a metal ion modeling tutorial which may help you: http://ambermd.org/tutorials/advanced/tutorial20/index.htm <http://ambermd.org/tutorials/advanced/tutorial20/index.htm>.
This is a tutorial for ion modeling using the bonded model by taking advantage of the MCPB.py program: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
This is a tutorial for ion modeling using the restrained nonbonded model: http://ambermd.org/tutorials/advanced/tutorial20/rnb.htm <http://ambermd.org/tutorials/advanced/tutorial20/rnb.htm>, before you checking it, you need to check the MCPB.py tutorial first: http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm <http://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.htm>.
This is a tutorial for ion modeling using the nonbonded model: http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm <http://ambermd.org/tutorials/advanced/tutorial20/nonbonded_model.htm>.
Hope it helps,
Pengfei
> On Mar 22, 2018, at 2:48 PM, Thomas Pochapsky <pochapsk.brandeis.edu> wrote:
>
> I am trying to modify a metal cluster to have two discrete waters
> solvating a ferrous ion in Xleap. What .lib and frcmods should be in
> leaprc to get the parameters I need?
>
> Thanks,
> Tom Pochapsky
>
>
>
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Received on Mon Mar 26 2018 - 10:00:04 PDT
