[gmx-users] Ligand covalently bound to protein: Best practice

[Ebert Maximilian]

Hi there,

I am about to setup a protein ligand complex in which the the amino acid is covalently bound to the ligand. What I was about to do is to build an artificial amino acid (in this case serine) with the ligand attached to it an derive partial charges using antechamber or the RED server. Then while preparing the force field in GROMACS I would treat the serine was a new residue type with the new FF information. Is the a good practice? 

Thanks very much,

Max