Re: [AMBER] planarity issue during md

From: David A Case <>
Date: Thu, 18 Jun 2020 08:11:16 -0400

On Thu, Jun 18, 2020, Sofia Vasilakaki wrote:

>About the atom types, carbon atoms in thymin in dna are not aromatic and
>have an sp2 atom type, same with my molecule.
>I run a dna minimization (amber tutorial1) and I did not notice any
>planarity issue. But again, the atom charges are not so different like the
>ones I generated in gaussian for my molecule.

I would not have thought that charges would have much to do with ring
planarity. I'm guessing that you will have to post an actual small
example that illustrates the problem, so that we can reproduce it.

Or, you could use parmed to examine all of the dihedral parameters in
the ring atoms: do they all have 2-fold torsions with a force constant near
10? Pay particular attention to the dihedral parameters involving the
pyramidal nitrogen.


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Received on Thu Jun 18 2020 - 05:30:05 PDT
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