Re: [AMBER] planarity issue during md

From: Sofia Vasilakaki <>
Date: Thu, 18 Jun 2020 12:58:09 +0300

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 attach a pic with this part of my molecule after a short min in solvent.

Thank you

> On Mon, Jun 15, 2020, Sofia Vasilakaki wrote:
>>I assigned atom types with antechamber and I used ff12SB.
> Check the atom types you have versus those in thymine itself: is
> anything different?
> Is your modified thymine less planar than you would get with a similar
> simulation of thymine itself?
> It's still not clear how big a deviation you are seeing; nor what
> happens upon minimization.
> ....dac
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(image/png attachment: min1.png)

Received on Thu Jun 18 2020 - 03:00:03 PDT
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