[gmx-users] Question Regarding Ligand-Enzyme Complex

Berk Hess gmx3 at hotmail.com
Mon Jan 21 15:50:48 CET 2008


In my opinion the Dundee server produces unreliable charges.
Also it only works for the oldest force field supported in Gromacs.
To obtain proper charges you will have to look in the literature
and if nothing is there, derive charges from quantum calculations
in a way that is compatible with one of the force fields supported
by Gromacs.


> Date: Mon, 21 Jan 2008 09:30:20 -0500
> From: mzottola at gmail.com
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Question Regarding Ligand-Enzyme Complex
> 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.
> Mark
> 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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