[gmx-users] topology file error
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
> 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
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.
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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