[gmx-users] question about ligand

Xiang Mao swallowswift at gmail.com
Thu Jan 29 20:09:14 CET 2009

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

Best Regards,

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