[gmx-users] Question Regarding Ligand-Enzyme Complex

[Mark Zottola]

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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