Re: [AMBER] planarity issue during md

From: David A Case <>
Date: Mon, 15 Jun 2020 14:51:16 -0400

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.


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Received on Mon Jun 15 2020 - 12:00:04 PDT
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