[AMBER] Developing Parameters for Bad Atom Types

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Mon, 9 Aug 2021 10:15:35 -0400

Dear Amber Community,

MM-GBSA is returning a “bad atom type” error because my system includes Au atoms— I’m looking at a protein-Au surface system, and previously, the below publication used the MM-GBSA approach to assess initial protein-surface docking poses (https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.5b02746 <https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.5b02746>).

I know how to add the parameters to the mdread2.f90 file and how to recompile the code afterwards. I just don’t know where I can find the appropriate parameters, or how I can compute them, for Au. I’d greatly appreciate any suggestions.

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Received on Mon Aug 09 2021 - 07:30:02 PDT
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