Re: [AMBER] Why SANDER can't rotate the dihedral for some angles? [Metal Center]

From: David A Case <>
Date: Mon, 3 Jan 2022 10:27:33 -0500

On Sun, Jan 02, 2022, Erdem Yeler wrote:

>I am trying to parameterize a molecule containing transition metal. During
>scanning, the sander could not rotate dihedral in the range of 80-160
>degrees and produced the same energy (See the chart below).

It would help if you provided the exact instructions you gave to sander.
The plot shows similar (not "the same") energy for angles in the 80-160
degree range. Do you know that this is wrong?

>It hardly turned some dihedrals at all.

It would help a lot to know details here: which dihedrals worked, and which
were problematic? Depending on the coordination number about the metal, it
can be quite tricky to scan about metal-based dihedral angles. But one
would need to more more information than just "it didn't work" to provide
useful suggestions.


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Received on Mon Jan 03 2022 - 07:30:02 PST
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