[gmx-users] situation where ligand is connected to amino acid

Justin Lemkul jalemkul at vt.edu
Wed Jan 3 02:04:48 CET 2018

On 1/2/18 2:59 PM, MD wrote:
> Hi Gromacs folks,
> I want to simulation a protein complexed with a ligand. However, the
> protein covalently bonded with the ligand via N-C bond. The ligand has a
> size of 27 atoms. The solution I could think of now is to create a modified
> amino acid which includes both the amino acid side chain and the connected
> ligand in rtp and make modifications in ffbonded.itp accordingly.
> I wonder if there is another route to get this done?

Your approach is correct.



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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