Re: [AMBER] missing bond parameter for Mg ion

From: Chen, Wei <>
Date: Tue, 30 Jul 2019 22:04:32 +0000

This looks great! Thank you!

Best Regards
Wei Chen

Physics, UIUC

On Tue, Jul 30, 2019 at 7:53 AM David A Case <<>> wrote:
On Mon, Jul 29, 2019, Chen, Wei wrote:
>I am trying to set up simulations for KRAS (using PDB id: 5vq2) with
>tleap. Since the protein comes with Mg ion and GTP, I used the force
>field for Mg and GTP from the contributed parameters database.

I'd recommend using GTP from that site, but the Mg2+ parameters that are
automatically loaded with whichever water model you choose: that is,
"source leaprc.water.xxxx" and you will automatically get Mg2+
parameters that are recommended for that water molecule.

Be sure that you have a TER card in your input PDB file between the
protein, GTP and Mg2+ residues.

>Could not find bond parameter for: CT - MG

This indicates that the system things there should be a bond between MG
and some carbon atom of type "CT". You will want to use a non-bonded
model for the MG. If adding appropriate TER cards doesn't help, we'd
need to know more about exactly what commands you gave to tleap.


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Received on Tue Jul 30 2019 - 15:30:02 PDT
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