Re: [AMBER] Clipping radius in AddToBox

From: David A Case <>
Date: Tue, 8 Jan 2019 09:07:09 -0500

On Tue, Jan 08, 2019, Lucas Bandeira wrote:
>Could one help me with the term "clipping radius". What it exactly means
>and how can I find the right values for protein atoms and for solvent atoms
>( -RP and -RW in AddToBox).

This is not definitive, but I always use RP of 2.5 and RW of 2.8 for
either waters or monatomic ions. I remember that years ago I played
around with these values (and you can experiment as well), but I don't
seem to be able to find the record of how I arrived at these values....

If you are adding bigger solvent molecules, you will probably have to
experiment some: see the Reference manual for suggestions.

[Dave: should we not add some defaults, and suggested values (maybe
different than those above) to the Manual?]


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Received on Tue Jan 08 2019 - 07:00:02 PST
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