Dear All:
How are you.
Sorry to bother you. I am trying do use gromacs to do MD on a protein-
ligand complex. I am following Dr. Kerrigan's tutorial on simulation of
protein-ligand complex. Here I have a question about the topology of
ligandgenerated by
prodrg. And when I run pdb2gmx on my protein(with gmx force field), I
noticed hydrogens were added to benzene rings. But when I look at the itp
file and pdb file with polar H generated by prodrg, I noticed there are no
hydrogens added to benzene ring of my ligand. I am just wondering if this
will affect the simulation, and what I should do. Thank you so much for your
help.
Best Regards,
mao
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