AMBER Archive (2004)

Subject: Re: AMBER: RESP partial charge calculation

From: FyD (
Date: Tue Aug 10 2004 - 12:46:16 CDT

Dear Sebastian,

> I am trying to calculate the RESP charge for an heme group with Fe+3.
> I would like to know which is the number I have to consider for Fe+3 in
> the RESP input file. I have used a complete basis set in the ESP
> calculation, so I have considered all the electrons for Fe, but I do not
> know if the number in RESP input must be 26, that is the Fe atomic
> number or 23, that is the actual total number of electrons in Fe+3. The
> same happends with other ions, like the O in a negative charged
> carboxilate group -C=O. Have I put 9 or 8 corresponding to the O atom in
> the RESP input file?

See below

> RESP assumes the ESP file is from an ALL electron calculation.
> I don't remember any 6-31G* all electron basis set for Fe so
> maybe you are using a pseudo potential for the Fe? If so,
> you must use the actual number of electrons on the Fe atom
> instead of the atomic number in the RESP input.

The 6-31G* basis set is available for up to Z = 36 in GAMESS/Gaussian
see V.A.Rassolov, J.A.Pople, M.A.Ratner, T.L.Windus
J.Chem.Phys. 109, 1223-1229(1998)
or at least up to Z=25...
I was also surprised to find such basis set available in GAMESS/Gaussian for
iron when we wrote R.E.D.-II... I guess it is because this work was written in

> > I am trying to calculate RESP partial charges for a heme-Fe+3 system.
> > I have previous calculate de electrostatic potencial using gaussian:
> > BLYP/6-31G* scf=(tight,maxcyc=500) pop=(mk,readRadii) # IOP(6/33=2). The
> > readRadii item was added to include the Fe radii of 0.49 since it
> > doesn't appear in the default library.

Yes, you have to do by this way for Gaussian. On the contrary, GAMESS seems to
use 1.8 as default value for such elements. See below... But I am suprised by
your value of 0.49... Is it not too small ? I would use at least 1.8 as in

and see also

> > After that I have built the correspondings input and espot files to run
> > the RESP program.
> > I have otained very high charges for certain C and H! Charges like -15
> > aren't reasonalby..., and in atoms far away from the Fe! Could anybody
> > help me to know if there is something wrong in using the RESP program
> > with a system that has an Fe atom?

Here are some information for your problem:
GAMESS handles atom radii as follows:
Z = 1-17 the radii of Kollman/Singh/Merz
Z = 19-35 the radii seem to be fixed to 1.8 and from what I understand if you
want to modify this '1.8' value you have to modify the file 'prplib.src' in the
source code and recompile.

Gaussian handles atom radii as follows:
Z = 1-17 the radii of Kollman/Singh/Merz
Z = 19-34 the radii are unknown and you have to provide the atom radii as you
Z = 35 radii = 2.3, where does it come from ?

In R.E.D.-II, RESP charges for elements up to Z = 35 are now automatically
handled. It is coded in a very simple way: We decided to apply the GAMESS way
for the elements Z = 19-35 for Gaussian by default. However, it has been written
in a way that you can very simply modify R.E.D.II to put your own value...

If you want I can provide you R.E.D. II, otherwise it is going to be released
beginning of September... With R.E.D. II you will be also able to associate
multi-conformation and/or multi-orientations for your heme molecule, to use
Gaussian optimization in GAMESS MEP computation (and vis-versa) and you
can also automatically generates non-standard RESP inputs and then performed
non-standard RESP fits...

Best regards, Francois

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