> I want to calculate partial charges for nanotube capped with amino acid. I
> use DFT calculation when it is just nano tube with out any amino acid. As
> far as i know the amino acid partial charges for AA in amber99 are
> calculated by HF/6-31G* RESP calculation.
> If i use DFT calculation for optimizing and calculating partial charges for
> nanotube- amino acid system, would amino acid partial charges be wrong or
> overstimated? I want to use this structures an an input for MD simulations
> in GROMACS using amber99 ff.
Concerning using HF vs DFT computation, or generating molecular
fragments for AA, or performing chemical equivalencing for
functionalized nanotubes, I would use PyRED at RED Server Dev. at
http://q4md-forcefieldtools.org/REDServer-Development/.
