Re: [AMBER] PSF file generation for heme and hydrogen peroxide

From: David A Case <>
Date: Thu, 13 Dec 2018 08:25:10 -0500

On Thu, Dec 13, 2018, 임호철(대학원/일반대학원 생명과학부(생명공학)) wrote:
>I would like to simulate catalase proteins which have heme d and hydrogen
>peroxide, with AMBER. I use VMD to make psf (protein structure file) from
>pdb, but I could not find topology file for heme and hydrogen peroxide.

Is there a reason that you want to first make psf files, then convert
them to Amber? Why not just build the catalase system in Amber, if you
intend to carry out the simulation in Amber?

If you intend to have the peroxide bound to the heme iron, that will
require some special care in parameterization (whether you use charmm or
Amber building procedures.) The MCPB (metal center parameter builder)
program is probably the best way to approach this in Amber.

...good luck...dac

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Received on Thu Dec 13 2018 - 05:30:02 PST
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