Re: [AMBER] conversion of tripose mol2 to amber type

From: David A Case <>
Date: Tue, 4 Aug 2020 21:37:09 -0400

On Tue, Aug 04, 2020, Nikhil Maroli wrote:

>I am new to the amber tool.
>I have a graphene oxide sheet consists of 2500 atoms in tripos mol2 format.
>How I can convert it to amber/antechamber out type?

This is by no means a simple task: Amber is set up mainly to work with
(bio)-polymers, and antechamber works at the single residue level. But
graphene and graphene-oxide sheets don't fit into this paradigm.

If you do a Google search "on graphene oxide Amber force field", there are a
number of hits that look pretty promising. You can see how they approached
this or similar problems.

Or, maybe someone on the list can chime in with advice here: people have
simulated surfaces and sheets with Amber, in spite of what seem like


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Received on Tue Aug 04 2020 - 19:00:02 PDT
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