[gmx-users] atom charge in new residue

Erik Lindahl lindahl at sbc.su.se
Mon Nov 1 17:37:01 CET 2004


Andrey is indeed right in that you can discuss the quality of various 
charge models a lot :-)

Merz-Kollman is probably the simplest "standard" QM protocol for fairly 
accurate charges, but for the cases I've run (lipid headgroups) CHELPG 
actually produced almost identical values. You can also argue that 
since CHELPG was used for the rest of OPLS-AA (with some constraints to 
get building blocks) that's the preferred method for this case at 

The other thing to consider is that QM charges _will_ vary between 
different conformations of the molecule, and that change can often be 
larger than the difference between Merz-Kollman, CHELPG or RESP.

However, no matter which model you choose it's likely going to be 
significantly better than Mulliken or old empirical (read guessed) 



On Nov 1, 2004, at 5:17 PM, Andrey V. Golovin wrote:

> Good question =)
> HF/6-31** and RESP doesn't really best choice :
> cite : "Overall, however, we have found these charge models (ESP and 
> to be quite useful for modeling biomolecular systems. The alternatives
> usually involve either (1) models such as Mulliken charges which do not
> necessarily reproduce the molecular electrostatic potential or (2) 
> empirically
> derived charges such as those fit to reproduce interaction energies and
> distances (CHARMM) or liquid properties (OPLS)."
> http://amber.scripps.edu/doc6/html/AMBER-sh-19.4.html
> As I noticed RESP charges for DNA/RNA is about twice bigger than OPLS
> one. But in case of pure DNA/RNA md with RESP charges are good. But for
> complexes i still have no pure answer. Something about CHELPG charges
> for OPLS was mentioned above. You can find it in mail-list
> http://www.gromacs.org/pipermail/gmx-users/2003-September/006975.html
> http://www.gromacs.org/pipermail/gmx-users/2002-November/003232.html
> Maximiliano Figueroa> Hi. I am created a new residue for OPLS, but I
> have a problem, I don't
> Maximiliano Figueroa> have a charge for each atom. I believe that the
> charge must be
> Maximiliano Figueroa> calculated with RESP, and with de basis HF/631
> G**, but, is that
> Maximiliano Figueroa> true?. If yes, somebody know a server that can
> calculate this partial
> Maximiliano Figueroa> charge in each atom at a new resiue?
> Maximiliano Figueroa> Thanks
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> Best regards,
> Andrey                          mailto:golovin at genebee.msu.su
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