Re: [AMBER] NAB superimpose issue

From: David A Case <>
Date: Tue, 8 Jun 2021 13:07:03 -0400

On Mon, Jun 07, 2021, Mandar Kulkarni wrote:
>superimpose( m_align,"1,10" , m_ref, "5,6");

The second and fourth arguments to superimpose should be atom expressions,
not just strings. Atom expressions have three subsections, separated by
colons. The superimpose command requires that the two atom expressions
return the same number of atoms, and that the two atom lists should be
matched in an ordered fashion. If the two molecules are not chemically
identical, one has to be very careful in choosing atom expressions that have
the correct number of atoms in the correct order.

I think what you are looking for is a setframe/alignframe pair: that will
align two molecules together in a way that can work even when they have
different chemistries.

...hope this helps...dac

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Received on Tue Jun 08 2021 - 10:30:02 PDT
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