[gmx-users] Question Regarding Ligand-Enzyme Complex

[David Mobley]

For what it's worth, I seem to recall that the ProDrg server itself
warns rather strongly about the charges being unreliable, and I
definitely agree with Berk here.

My favorite approach for modeling small molecules is to  use the AMBER
GAFF small molecule force field in combination with one of the AMBER
protein force fields (there are ports for gromacs). The Antechamber
package provides a fairly straightforward way to compute sane partial
charges for relatively arbitrary small molecules in an automated and
fast way.

I should really put a tutorial together on this. But unfortunately I'm
too swamped at the moment. If anyone wants to volunteer to put
together a tutorial, I can provide the web space and some guidance on
the steps involved.

Best wishes,
David


On Jan 21, 2008 6:50 AM, Berk Hess <gmx3 at hotmail.com> wrote:
>
>
> Hi,
>
> 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.
>
> Berk.
>
>
> > 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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