[gmx-users] Question about scaling charges

David Mobley dmobley at gmail.com
Fri Sep 1 16:50:31 CEST 2006


You might want to start by reading something basic on how force fields
work, i.e. in Leach's Molecular Modeling book, or maybe Jay Ponder's
recent "Force Fields for Protein Simulation" review (available on his
web page here: ftp://dasher.wustl.edu/pub/papers/advprotchem-66-27-03.pdf).

I am not too sure what you mean by scaling, and the answer to your
question probably depends on the force field you want to use.
Basically, you need to use charges that are "appropriate" for the
force field you are using. For example, it would probably be unwise
for me to use, say, some sort of QM with Mulliken analysis to get
charges for the partial charges on a ligand to use in a protein for
which I use AMBER parameters, since the AMBER partial charges come
from SCF 6-31G* RESP fitting, and Mulliken charges won't "match" well
since they are very different from what the force field was
parameterized with.

So, how I would go about answering your question, if I were you, is
figure out what force field you plan on using, and then figure out how
the "normal" partial charges (i.e. protein partial charges) for that
force field were assigned, and then do something similar to get the
partial charges for the molecule you are trying to parameterize. You
of course need to do something similar with the other parameters, as

Again, the basic message is that you need to come up with
"appropriate" parameters that match well with the force field you are
using, which usually means you need to do something similar to what
was done to parameterize the force field.


On 8/31/06, Arthur Roberts <aroberts99163 at yahoo.com> wrote:
> Hi, all,
>      I was talking to a friend of mine that works in
> an MD lab.  He said that the charges from QM/MM or
> semiempirical need to be scaled to charges in the
> force field.  For example, a heme will have specific
> charges in the force field, while hemes that represent
> different bound states may have a different charge
> distribution, depending on which method is used to
> calculate it.  Let us say that the force field charge
> is +1 for simplicity and the charge is +2 by using
> other methods.  The scaling would suggest that you
> would reduce the charge of the heme by one half, so
> that it would be compatible to the force field.
> However, this doesn't make sense to me, since partial
> charges should always be related to an electron and
> therefore, in principle, should never have to be
> scaled.  I would appreciate anyone's input on it.
> Best wishes,
> Art
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