[gmx-users] Protein-ligand

[P.R.Anand Narayanan]

Dear Gromacs users,
I am planning to bind a ligand to a protein and use gromacs to run the simulations. But for using the pdb2gmx command, i heard we have to remove all the ligands and cofactors associated with the protein. While pasting the necessary parts of the ligand into the gro file, i heard that the bonds would be broken. Is this true? and if yes are there methods to run the pdb2gmx command with the ligand. Or the same command without the ligand but not breaking the bond after pasting it back.
Pls help

Anand



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