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Subject: RE: [NWCHEM] Partial atomic charges
Date: Tue, 20 Mar 2007 10:33:11 -0700
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From: "Straatsma, T P" <tps@pnl.gov>
To: "Francesco Pietra" <chiendarret@yahoo.com>,
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For AMBER the procedure to get partial atomic charges if HF/6-31g*
followed by RESP fitting. Two-stage RESP is available in NWChem and
avoids the CHELPG limitation you mention.
For effective MD you should break your molecule into segments.  

Dr. T.P.Straatsma, Associate Division Director 
Computational Biology and Bioinformatics 
Pacific Northwest National Laboratory 
P.O.Box 999, MSIN K7-90
Richland, WA 99352 
Tel. (509) 375-2802 
Adm. (509) 372-4623 
Fax (509) 372-4720
<http://cisd.pnl.gov/csm/technologies/comp_biology.stm#> 

-----Original Message-----
From: owner-nwchem-users@emsl.pnl.gov
[mailto:owner-nwchem-users@emsl.pnl.gov] On Behalf Of Francesco Pietra
Sent: Tuesday, March 20, 2007 10:01
To: users nwchem
Subject: [NWCHEM] Partial atomic charges

I am setting up classical (Amber FF) simulations on natural products,
where the "fragment" is the final "sequence" approaching the limit of 99
atoms.
Difficult, if possible at all, to cut the molecule into fragments.

In learning about the method used to define the partial charges, I came
across a discouraging (for my type of job) description:

"One of the weak points of CHELPG (and other approaches based on fitting
the MEP) is the treatment of larger systems, in which some of the
innermost atoms are located far away from the points at which the MEP is
evaluated. In such a situation, variations of the innermost atomic
charges will not lead to significant changes of the MEP potential
outside of the molecule and fitting of these atomic charges will
therefore not result in meaningful results. It should also be remembered
that atomic charges can depend strongly on the conformation of the
molecule.
Representative atomic charges for flexible molecules should therefore be
derived as average values over several conformers. Using ethanol as an
example, the charge parameters derived for the Cs symmetric conformer A
and the C1 symmetric conformer B vary, in part, by almost 30%. The
variation is, however, rather different for different parts of the
system(http://www.cup.uni-muenchen.de/oc/zipse/compchem/pop/chelpg.html)
"

At any event, for a given novel fragment (geometry optimized with MM
global space search), should the RHF-ESP calculation be preceded by a
RHF-Geometry calculation?

I rely on Ecce for the ESP calculation, though it seems to me that the
question I posed is valid also for using NWChem directly.

Thanks
francesco pietra

 
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