[gmx-users] topology file error

[Justin Lemkul]

On 2/19/18 5:55 AM, spss4 at iacs.res.in wrote:
> Hii all
> I have prepared the topology file for urea molecule in AMBER99sb-ildn 
> force
> field taking the parameters from ffbonded.itp and  ffnonbonded.itp
> available in AMBER folder. After simulation the urea molecule is somewhat
> distorted. The N-H bond is tilted. Please suggest me how to solve this
> problem.

What does "tilted" mean and why do you think it's a problem? The 
molecule won't remain exactly planar all the time.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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