Mark Zottola wrote:
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?
All of the above is predicated on your choice of "force field" as a
model of physics. That server you mention produces topologies in a
manner (apparently - I know nothing about it) consistent with one such
force field. The primary source of information about it is the
publication in which they announced it. You should read about how it was
developed, and what method that server uses, and form your own
conclusions. Also, see here
http://wiki.gromacs.org/index.php/Parameterization
Mark
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