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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