Re: [AMBER] torsion angles of carbon allotropes

From: David Case <>
Date: Tue, 9 Oct 2018 01:04:27 +0000

On Mon, Oct 08, 2018, Ibrahim Said wrote:

> I built one of these carbon structures with hydroxyl groups and optimized
> it with Gauss-16. I then used these structures as ligands for a protein. In
> leap suite, I got only 22 warnings. When I saved both prmtop and inpcrd
> files, I got the following message
> 1-4: angle 2862 2898 duplicates bond ('triangular' bond) or angle ('square'
> bond)

This should not be a problem, pre se. It means you have cyclopropane
or cyclobutane like entities in your structure.

> The problem is during minimization, steepest descent is only working and

I think we'd have to know more about what is going on: why do you say
that only steepest descent is working? It may be that you don't have a
very well-minimized structure, but I have very little to go on.


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Received on Mon Oct 08 2018 - 18:30:03 PDT
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