One short question:
after integration of the chromophore into the protein (making 2 peptide
bonds of this residue with N and C termi of adjacent protein's residues)-
I've noticed that total charge of my system has been decreased from 0 to
-1. Assuming that both chromophore and protein had neutral charges why
qtotal have been reduced after its joining ?
James
2014-05-19 16:06 GMT+04:00 Marc van der Kamp <marcvanderkamp.gmail.com>:
> Hi James,
> See brief answers below.
>
> 1) What the information from the initial ff parameters of my QM group taken
> > from the prmtop would be most meaningful for the qm/mm simulation.
> > Previously you've mentioned that this information will be ignored during
> > qm/mm run but it seem that initial molecular 3D geometry and charge
> > distribution have some matter, haven't it?
> >
> > As mentioned before, only the MM parameters of QM atoms should matter.
> Of course, the coordinates (3D geometry) matter too.
> MM force-field charges will be ignored (as will the bonded MM terms) for
> the QM atoms.
>
>
> > 2) What are the most reasonable methods and tools for the analysis of
> QM/MM
> > trajectories ? On what dynamical properties of simulated system should I
> > paid most of attention? E.g the most trivial is the analysis of the 3D
> > geometry during simulation. How can I make such analysis obtaining both
> > visualization and numerical values (E.g torsion angles in
> > functional-relevant groups)? Does it possible to calculate charge density
> > for those groups as well?
> >
> > What you want/need to analyze depends on your system/your questions;
> tools
> etc. are the same as used for pure MM.
> This thread (about QM/MM) is not the right place to go into this. First
> check the available manual (e.g. of ptraj & cpptraj) and tutorials.
>
> If you want to get the position of link atoms, you need to use the writepdb
> option in the sander input file, see manual for details.
> You can print Mulliken charges of the QM atoms to get an idea about the
> 'charge density' (see under sqm in the AmberTools manual).
>
> Hope this helps,
> Marc
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Received on Thu May 22 2014 - 03:30:03 PDT
