[gmx-users] topology file error

Justin Lemkul jalemkul at vt.edu
Mon Feb 19 13:56:13 CET 2018

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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