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

MD refmac5 at gmail.com
Tue Jan 2 20:59:40 CET 2018

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?



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