>
> The conclusion here seems to go back to the original point: if both QM
> and MM regions are non-neutral, the QM/MM calculations are problematic. If
> the QM region includes NADH (net charge= -2) and the ligand, reducing the
> qmcut even to 0 cannot solve the issue in our case. The huge charge
> transfer and polarization components between NADH and the ligand, during
> the complex forming stage, still creates extreme electrostatic values.
Henry, what is your definition of being problematic - is the SCF not converging? - which means anything calculated from that is incorrect. Or is the QM calculation working but the ultimate GBSA binding result is coming out incorrect?
The QM code should support running simulations with non zero charges (although the QM region requires an integer number of electrons). Are you setting the charge correctly in the QM calculation? - I could see how enforcing the charge to be zero but including 2 extra electrons could cause all sorts of problems.
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Associate Research Professor |
| San Diego Supercomputer Center |
| Adjunct Associate Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Apr 03 2015 - 16:00:02 PDT
