On Mon, 2014-05-12 at 10:54 +0100, Hannes Loeffler wrote:
> On Fri, 9 May 2014 15:49:27 -0400
> David A Case <case.biomaps.rutgers.edu> wrote:
>
> > On Thu, May 08, 2014, hannes.loeffler.stfc.ac.uk wrote:
> >
> > >
> > > So, the following name list does converge the structure.
> > >
> > > &qmmm
> > > qm_theory='AM1',grms_tol=0.0002,tight_p_conv=0,
> > > scfconv=1.0d-9,itrmax=500,pseudo_diag=1,vshift=0.1,
> > > ndiis_attempts=200,ndiis_matrices=6,maxcyc=2000,
> > > qmcharge=-1,verbosity=1
> > > /
> >
> > Thanks for the info: we should probably be suggesting use of vshift
> > more prominently in the case of convergence problems.
> >
> > >
> > > Except that the structure gets "folded" (see attachment) with the
> > > carboxy groups contacting the amino groups.
> >
> > I suspect that these odd geometries are related to convergence
> > problems. Your initial geometry converged fine, but after some steps
> > of minimization, which probably involved some "folding", you ran into
> > problems.
>
> I have attached a NetCDF trajectory which shows what is going on during
> geometry optimisation. The practical problem is that there is no way to
> control this.
>
> I have also attached the trajectories for two very similar structures,
> ZINC03814826 and ZINC03814838. In ZINC03814826 one carboxylate group
> abstracts a proton from an amino group at the far-end of the
> molecule (the same happens in ZINC03814828 at HF/6-31G* with g09). The
> molecule adopts an extended structure at the end of 2000 steps (not
> converged to grms). In ZINC03814838 the two carboxylate groups appear
> to get "decarboxylated".
Yuck. I would guess that you're right in that this is a limitation of
using gas-phase structures in charge derivation. (I believe such
zwitterions are only stable in solution.)
A relatively simple alternative I can see would be to use some kind of
implicit solvent model (either GB in sander or PCM/COSMO in Gaussian)
when you minimize before using the standard HF/6-31G* Merz-Kollman
scheme to get the partial charges.
Of course the real issue is working this into a reliable, automated
workflow...
All the best,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon May 12 2014 - 04:30:03 PDT
