Hi All, I am trying to get pdb2gmx -vsite h to work for a sugar attached to my protein. I am using non standard atom names to differntiate from the OPLS atom names. I have gone through the manual a few times and I don't understand the relationship between the files. The ffoplsaa.ddb has bonds between heavy atoms and not hydrogens. Why?
Thanks, Ilya -- Ilya Chorny Ph.D.
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