AMBER Archive (2005)

Subject: Re: AMBER: Cu++ and RED

From: FyD (fyd_at_u-picardie.fr)
Date: Sat Mar 12 2005 - 16:00:56 CST

Dear Cenk Andac,

> Manual says I have RED-I. Perhaps RED-II can handle my
> problem. Where can I get RED II?

You _must_ use R.E.D.-II for third row elements of the periodic table. You will
find some information in the R.E.D.-II manual about K-Br elements and RESP/ESP
charges. I will send you R.E.D.-II in a personnal email. With R.E.D. II you can
get the ESP/RESP charges for molecules having a multiplicity different from 1
which is particular useful for metal complexes.

Here is what you can find in the R.E.D.-II manual:

Page 4: In R.E.D. II (version 2.0), we implemented the multi-conformation RESP
and ESP fit that can be automatically carried out for a well-defined set of
molecular conformations. Thus, 'multiconformation' and 'multi-orientation' RESP
fit can be performed together or independently according to the user choice.
'Standard' but also 'non-standard' RESP inputs can now be generated. The output
from geometry optimization generated by one of the two QM programs can be used
as input for MEP computation using the second QM program. Finally, RESP and ESP
charges can be derived for chemical elements up to Z = 35 (Z is the total number
of electrons).

Page 16: The use of Cartesian or spherical harmonic functions for the basis set
functions is another example of differences between the algorithms of the
''GAMESS'' and ''Gaussian'' programs. Particularly, such differences are
observed for the third row elements of the periodic table. With R.E.D. II, the
derivation of RESP or ESP charges for chemical elements having a total number
of electrons up to Z = 35 is now possible. Thus, to allow the derivation of
highly reproducible RESP charges for complexes containing metal atoms (Sc-Zn),
spherical harmonic functions removing contaminant Cartesian functions are used
within the two QM programs. Thus, the ''ISPHER = 1'' (for ''GAMESS'') and
''5D'' (for ''Gaussian'') keywords are used in the geometry optimization and
MEP inputs if a third row element is detected in the studied molecule. In this
case, the default algorithm available in these QM programs is not used (See
lines 510, 511, 916, 917 & 545, 546, 970, 971 in the R.E.D. source code to
modify this feature).

- Once you got R.E.D.-II, I would read the manual & try to simplify your
problem. I mean do _not_ execute the Geom. opt. using R.E.D. but in a
"standalone mode", and then, once you got your optimized QM output, load it as
input in R.E.D.-II as it is described page 27 in the tutorial.
- I would also find out what is the multiplicity of Cu2+ and the number of
ligands expected for a total chnage = 0 or = +2: I have no idea...
- I would calculate ESP charges in a 1st step replacing the HF/STO-3G theory
level by the HF/6-31G* one in the MEP computation (the R.E.D.-II code has to be
slightly updated; this case will be automatically handled in R.E.D.-III) using a
unique molecular orientation and look at the charge values you get. The atom
equivalencing is performed at posterio to the fit in this case and we already
observed that additional restraints can produce surprising/weird results...
- Then, you can try to calculate RESP charges and multi-orientation and even
multi-conformation if you wish...

I hope this helps, regards, Francois

  F.-Y. Dupradeau
DMAG EA 3901 & Faculte de Pharmacie, Amiens, France
The Scripps Research Institute, La Jolla, CA, USA
       --
http://www.u-picardie.fr/labo/lbpd/FyD.htm
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