[gmx-users] Question Regarding Ligand-Enzyme Complex

[Mark Abraham]

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