Re: [AMBER] Zinc Oxide and protein simulation with AMBER

From: David A Case <>
Date: Tue, 13 Dec 2016 10:34:53 -0500

On Tue, Dec 13, 2016, vivek m wrote:
> I want to perform molecular dynamics of (ZnO)12 cluster with a protein.
> I have drawn the ZnO cluster and performed gaussian optimization to get the
> correct geometry and charges. I have also performed docking of ZnO cluster
> with my protein. I have also done the protein preparation as described in
> the AMBER tutorials.
> I do not know how to move ahead from here. How do i prepare the ZnO-
> protein prmtop and inpcrd files.

See sections 15.7 and 15.8 in the Amber 2016 Reference Manual.


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Received on Tue Dec 13 2016 - 08:00:04 PST
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