On Mon, Feb 26, 2018, Rana Rehan Khalid wrote:
>
> My protein system have GTP and two Mg+2 ions, which have electrostatic
> interactions with two Aspartic acid Asp residues. How i can generate the
> force filed for this, can I generate the parameters for this metallic
> system by using Antechamber or i have to use MCPB.py for this. Kindly guide
> me Thanks.
My recommendation: get GTP parameters from the contributed parameters data
base (see the Amber web page for details). Use the magnesium ions that
are automatically loaded when you source a leaprc.water.xxxx file (you will
need to choose the water model you want.)
Of course, carefully monitor your structure in this region as the simulation
progresses. Magnesium interactions with pyrophosphates are generally quite
important, and you will want to use a good starting structure.
....good luck....dac
[After you some experience, you might wish to explore 12-6-4 magnesium
parameters. See the Amber Reference Manual for more details.]
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Received on Mon Feb 26 2018 - 15:00:04 PST
