[gmx-users] Question Regarding Ligand-Enzyme Complex

Mark Zottola mzottola at gmail.com
Mon Jan 21 15:30:20 CET 2008

I am following the tutorial given in the gromacs manual.  While it does have
a stepwise directions, there is a paucity of detail.  The Dundee server is
part of those directions.

You are right, charge derivation is part of forcefield development.  But
which forcefield does this server use?  And unless the forcefield is a fully
united atom forcefield, the highly positive charge on nitrogen makes no
sense.  And if it is a united atom forcefield - why add hydrogens?  If the
forcefield includes only polar hydrogens, why do amino protons on a
protonated NH2 group have a negative charge?

These issues are above and beyond a simple read of wth Wiki on gromacs.  So
I again ask what is going on RE: my previous post.


> 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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