Re: [AMBER] How to generate parameters for two MG 2+ ions ---GTP

From: Rana Rehan Khalid <>
Date: Thu, 1 Mar 2018 21:09:52 +0500

Dear Amber Users

How I can deal cGMP with same above mentioned system, is it force field are
available or I have to do some thing different to produced prmtop and crd


On Tue, Feb 27, 2018 at 3:55 AM, David A Case <>

> 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 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 Thu Mar 01 2018 - 08:30:03 PST
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