[gmx-users] OPLS-AA Charge Calculation
Nagy, Peter I.
PNAGY at UTNet.UToledo.Edu
Wed Aug 30 15:25:43 CEST 2006
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...)
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.
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
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
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
t.piggot at bristol.ac.uk
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