I usually use B3LYP/6-31G* SCRF=PCM to do geometry optimization and then
calculate ESP at HF/6-31G* level to be consistent with GAFF and some
biomolecular force fields.
Best
Junmei
On Sat, Oct 28, 2017 at 4:47 PM, Andreas Tosstorff <
andreas.tosstorff.cup.uni-muenchen.de> wrote:
> thank you both for your responses! which basis sets would you recommend
> using when using a solvent model? my understanding is that HF6-31g* tends
> to exaggerate polarization, which is why people use it when calculating
> charges in the gas phase to be then applied in MD in solution.
>
> Von meinem iPad gesendet
>
> > Am 28.10.2017 um 15:23 schrieb Junmei Wang <junmwang.gmail.com>:
> >
> > Good point. I encountered the same problem when I optimized
> amino-acid-like
> > small molecules using Gaussian. The optimizer in the recent Gaussian
> > versions can migrate proton from one heavy atom to another to neutralize
> > the molecule. The two atoms may be separated several bonds (the longest
> > distance is 7 bonds)! My solution was to use PCM to do optimization and
> > then did a single point calculation to calculate ESP. With PCM, the
> charge
> > centers are well kept.
> >
> > Best
> >
> > Junmei
> >
> > On Sat, Oct 28, 2017 at 8:16 AM, David A Case <david.case.rutgers.edu>
> > wrote:
> >
> >>> On Sat, Oct 28, 2017, Andreas Tosstorff wrote:
> >>>
> >>> Thanks a lot for the advice! The structure I have is that of the small
> >>> molecule bound to a protein. If I submitted this structure, without
> >>> further geometry optimization, wouldn’t that overstabilize the bound
> >>> ligand conformation?
> >>
> >> In principle, MD results should become independent of the starting
> >> configuration as sampling becomes more complete.
> >>
> >>> From the point of view of developing charges, many people prefer to fit
> >> several conformations at once, to get kind of an "average" charge set
> that
> >> works pretty well for many conformations. The ways in which those
> >> conformations are generated is outside the scope of antechamber/resp.
> >>
> >> You might try adding a cosmo solvation model to the Gaussian run, then
> >> optimizing. The will probably stabilize the zwitterionic form. Or,
> >> minimize
> >> the molecule in a force field, since that is what you will be using for
> the
> >> binding calculation anyway. (This is iterative: get charges for
> >> the conformation you have, minimize in ff, re-determine charges from
> this
> >> minimized conformation, see if they have changed very much.)
> >>
> >> ....dac
> >>
> >>
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Received on Sat Oct 28 2017 - 18:30:02 PDT
