I have docked a ligand that contains a primary amino group to a protein. I want to use dynamics to study this complex. Following the tutorial, I used the dundee server to prepare the files for my ligand. When I examine the charges of the terminal amino group, the charge for the nitrogen is approximately +0.7 while the charge on the amino protons are all about -0.05. Since it seems the charges are unusual, I have several questions: 1) Where in the gromacs distro is the data for amino acids? 2) Should I expect the charges on those amino groups to be similar? 3) If the charges are out of whack, how does one do charge generation? Is there a reference for this? 4) Finally, how can I validate the atom types assigned to the ligand?
Thanks for the help. Mark
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