[gmx-users] OPLS-AA Charge Calculation

Jochen Hub jhub at gwdg.de
Wed Aug 30 17:43:27 CEST 2006

Nagy, Peter I. wrote:

> Dear Tom,
>      I read your e-mail in the gmx-users mailing list, and decided to 
> answer in a personal mail.
> (I am not eager to appear on that list...)

Why that?

>     In my opinion, your approach is basically correct. It is a matter 
> of consideration whether the
> RHF/6-31G* level for geometry oprimization is correct. Generally, for 
> a POSITIVELY charged
> closed shell system RHF/6-31G* may be acceptable. If the ion is 
> negatively charged, consideration of diffuse functions are needed. 
> What I normally do, I perform the optimization
> with both basis sets, and see if the geometry differs.
>    The next problem: do you want to study your molecule in the gas 
> phase of in solution? The HF/6-31G* optimization and charge derivation 
> was suggested by the Jorgensen group, because the dipole moment at 
> this level (optimization performed in the gas-phase) is exaggareted by 
> about 20% and this overestimation accounts for some polarization 
> appearing in solution. Thus this calculation may provide acceptable 
> charges for in-water calculations, but probably not for gas-phase or 
> in non-polar solution.
>    I noticed that you created the CHELPG ELPO map, and then 
> recalculated the charges with a
> RESP fit. I assume that the CHELPG and the RESP charges differ quite 
> remarkably. My recent
> experience is that the CHELPG charges provide too polar charge 
> distribution, and the RESP
> charges derived in this way may serve better. But if the two sets, 
> CHELPG and RESP differ
> too much, you would need an independent verification of the preference.
>   I am interested in this problem, and if you want you may write me in 
> a personal e-mail. We can
> further discuss the problem, and I could say more if having some idea 
> about your system. Also,
> B3LYP/6-31G* optimization may be an alternative and/or optimization in 
> solution using the IEF-PCM method. This may be discussed if you want 
> to continue this correspondence.
> Best regards
> Peter I. Nagy
> The University of Toledo
> Toledo, OH, 43606, USA
> ------------------------------------------------------------------------
> *From:* gmx-users-bounces at gromacs.org on behalf of TJ Piggot
> *Sent:* Wed 8/30/2006 8:21 AM
> *To:* gmx-users at gromacs.org
> *Subject:* [gmx-users] OPLS-AA Charge Calculation
> Hi all,
> I am trying to calculate partial charges of a ligand for the OPLS-AA/L
> forcefield. I have searched the mailing lists and literature and would 
> like
> to confirm that the approach i am going to take is a sensible and accurate
> one.
> Firstly i take an all atom structure of the ligand and minimise in
> gaussian03 using the RHF method and 6-31G* basis set (is this a suitable
> level of theory for my charged ligand of 43 atoms?).
> Then i calculate the electrostatic potential using the CHelpG method and
> output it on a grid.
> Then use a two stage RESP fitting to calculate the charges.
> Thanks for any input you have on this approach
> Tom Piggot
> ----------------------
> TJ Piggot
> t.piggot at bristol.ac.uk
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Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de

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