Re: [AMBER] query about Br

From: David A Case <>
Date: Tue, 24 Nov 2015 09:32:00 -0700

On Tue, Nov 24, 2015, Ayesha Kanwal wrote:

> CPQ is ligand of 1IMX protein and Br is another molecule. Should I
> treat it like ligand? And run antechamber again for it? Or what I have
> to do? Please show me some way.

You can treat Br like another ligand, but you don't have to run antechamber:
Amber provides an extensive set of monatoic ion parameters: see the "ions"
section in the Manual (section 3.9). Note that you must choose ions
parameters that match the water model you are using--there is no default here.

....good luck....dac

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Received on Tue Nov 24 2015 - 09:00:03 PST
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