VMD-L Mailing List

From: Pawel Kedzierski (pawel.kedzierski_at_pwr.edu.pl)
Date: Tue Apr 21 2015 - 03:04:32 CDT

Dear Brian,
W dniu 20.04.2015 o 21:18, Bennion, Brian pisze:
> Hello All,
>
> I have been parameterizing an overall positively charged molecule
> (scaling=1.1 not 1.16, DistanceWeight=0.8). Most of the compound was
> described with very minor penalties from the cgenff.paramchem.org server.
>
> When I start the charge optimization for the sections of the molecule
> that need more validation I am finding that a couple of the atoms are
> not converging in the MM calculations (objective function is > 1000 at
> the end of the optimizations).
>
> That is I two atoms for which the final distances in the MM
> calculations peg to the upper and lower shift boundaries. Increasing
> or decreasing these two values just moves the MMDistDelta to the new
> value that was set in the constraints section of the fftk window.
Rather as a general comment, if the QM minimum is shallow (e.g.
dominated by dispersion interactions) it may not exist in MM unless you
adjust the Lennard-Jones parameters, especially epsilon. But this would
apply to atoms with small charges and You have a charged system.
>
> I checked the qm log files that describe these two interactions and
> they terminated normally with no obvious error. I have looked at the
> structures from the log files and they appear to settle ok.
> I do note that for one of these two atoms, a nitrogen in (-C=N-O-),
> shows conflicting N...H-O-H distances. Loading in the gaussian log
> file, the converged distance is 2.46A. However, in the output from the
> chargeopt.log the QM distance is reported as 4.031A.

You should always check the structures in the GAU files generated by
FFTK before calculations. I find it quite common that the initial
position of water conflict with some other atoms of the parametrized
molecule. In many cases, you may tinker with internal coordinates of the
water in the GAU file to make this water point to some other direction.
Note that what is optimized in these jobs is only the distance and
rotation of this water, and the interaction at this optimized distance
should be dominated by the atom where this water is placed and not by
some other. I think that even positioning this water at some skewed
angle but further from other atoms is better than omitting such data at all.

It is also worth noting that FFTK is rather simplistic about what it
thinks is acceptor or donor atom. I would advice to check this, too.
Nitrogens for that example are by default considered acceptors but if
you have positive Mulliken charge at this nitrogen it most likely will
interact better with oxygen ot the water, so it should be put on the
"Donors" list in FFTK.
HTH,
Pawel

> One caveat is that the water in this particular interaction is
> relatively close to an intramolecular oxygen atom (hbond=2.18A.) I am
> not sure how much this is affecting the calculation at the N atom.
>
>
> Do I toss these data points out or is there something more subtle that
> I can do so solve this problem?
>
> Brian