Re: [AMBER] planarity issue during md

From: Sofia Vasilakaki <>
Date: Mon, 15 Jun 2020 17:33:55 +0300

It is not a deviation because it does not appear in some frames only.

I assigned atom types with antechamber and I used ff12SB.

I did not have this problem with planarity when I used the charges
generated with antechamber. The amide N there has a -0.46 charge and
bonded with a C atom of 0.49, while in Gaussian is -0.96 and 1.77.

I also got this amide N out of the plane when I simulated the molecule alone.

Thank you

> On Mon, Jun 15, 2020, Sofia Vasilakaki wrote:
>>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.
> How far out of planarity are they? How did you assign atom types and
> force field parameters?
> One expects some deviations from base planarity during an MD simulation.
> It's probably worth checking a minimization (of just the small molecule
> itself) in order to see what the lowest-energy conformation looks like.
> ....dac
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Received on Mon Jun 15 2020 - 08:00:03 PDT
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