On Sat, Nov 19, 2016, 杨满意 wrote:
>
> Now I wanted to use amber to do QM/MM (PM6/GAFF) MD
> simulation. Antechamber is designed to be used with the GAFF, which
> covers almost all the organic chemical space that is made up of C, N,
> O, S, P, H, F, Cl, Br and I. For my studied system, there are some
> other elements, such as Boron (B) and silicon(Si), in my solute. In
> MD simulation，we use QM(PM6) to describe the solute region and
> MM(GAFF) to describe the solvent region. When I use Antechamber
> tools to generated amber inputfile, there will be some ' ATTN, need
> revision' cards in the solute frcmod files. I want to konw how
> can I generated correct inputfiles(.iprmtop and .inpcrd ) files
> automatically.
You probably cannot do this automatically. Amber's QM/MM implementation
requires an MM force field for everything, even though it is not used for
QM/MM calculations. You can fill in the "need revision" lines with guesses.
The main things to be concerned with: you need correct masses for all atoms,
and good Lennard-Jones parameters. Also, the ideal bond lengths in the MM
force field are what is used for any bonds that are SHAKEN. Others on the
list may wish to chime in with things I may have forgotten, but that should
get you close.
There is a project underway to implement a "universal" MM force field, which
would simplify and automate this process. But that won't be available for a
while.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Nov 22 2016 - 05:30:05 PST
