Re: [AMBER] How to compute MM/PB(GB)SA with Extra Points

From: David A Case <>
Date: Mon, 31 Jan 2022 21:17:32 -0500

On Mon, Jan 31, 2022, Matthew Guberman-Pfeffer wrote:
>The tutorial on extra points
><> says,
> "With the addition of topology writing capabilities and a new format
> for encoding the extra points, these features of the system can start
> to become more permanent. The current master branch of pmemd and
> pmemd.cudasupport the upgraded topology format, and will be available to
> all users in Amber22. Users who need early access to this functionality
> should contact the developers.” [emphasis mine]

I don't even really understand what is being said here (cc-ing to Dave
Cerutti, the mdgx author.

This tutorial refers to "custom extra points", which are an extension
of (I guess "normal") extra points that have been supported by Amber for
more than a decade. But the distinction between new features and exsiting
ones is not explained. Things that are in the "current master branch" refers
to code under development. Asking people to "contact the developers" is
not all that helpful, as you have seen.

My personal opinion is that tutorials like this should only be posted when the
code is actually available (which, if the promise is kept, will be in
*AmberTools22*, not Amber22.) But Dave should see this email, and may be
able to help you out.


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Received on Mon Jan 31 2022 - 18:30:02 PST
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