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

[Justin Lemkul]

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

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

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