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