VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Mon Apr 20 2015 - 14:18:45 CDT

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.

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. 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