[AMBER] planarity issue during md

From: Sofia Vasilakaki <svasilak.chem.uoa.gr>
Date: Mon, 15 Jun 2020 10:23:42 +0300

Dear all,

I simulated a small molecule which contains a similar to thymine ring,
substituted by one C=O group. I generated partial charges in Gaussian.
During simulation the amide N and some of the carbon atoms of the ring are
not planar.

Is this acceptable? Is it problematic for the mmpbsa calculations ?

Thank you,

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Received on Mon Jun 15 2020 - 00:30:04 PDT
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