[gmx-users] How to define the covalent bonds between ligand and protein

[Bikash Ranjan Sahoo]

​Dear All,
   I am trying to perform protein-ligand MD where the ligand is covalently
bonded to the receptor. I have seen few earlier post from other users who
are trying to solve such complexes. Few days ago few gromacs users
suggested to define a new residue to the force fields. However, it is very
difficult to define the necessary parameters from PRODRG/Acpype/ATB. If
anyone define such systems using these servers output, kindly help me in
defining my ligand parameters for which I'll remain ever grateful to you.


Thanking You
In anticipation of your reply
Bikash
Osaka Univ. ; Japan