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

Bikash Ranjan Sahoo bikash.bioinformatics at gmail.com
Fri Dec 12 12:23:51 CET 2014

​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
Osaka Univ. ; Japan

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