Re: [AMBER] Putting oxygen molecules around protein structure

From: David A Case <>
Date: Thu, 12 Mar 2015 17:19:25 -0400

On Thu, Mar 12, 2015, Shukla, Saurabh wrote:

> I am trying to study a diffusion process inside a protein. I want to put
> 500 oxygen molecules outside the protein and want to simulate the system
> to see the trajectory of oxygen molecules in the protein cavities.
> Please suggest how I can go about putting oxygen molecules in the
> solvent. Is there any direct command to replace some of the water
> molecules by oxygen molecules? If not, which files would I need to
> change in order to introduce oxygen molecules in system?

The best way that I can see involves hand-editing your input pdb file, as
explained earlier:

You might use the addIons to get positions of ions, then manually change the
ions to oxygens. The file that needs to be changed is the input PDB file.

...hope this helps....dac

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Received on Thu Mar 12 2015 - 14:30:03 PDT
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