[gmx-users] Partial charges

[Alex]

This has got nothing to do with Gromacs.

A general comment: no, you should not neglect it. I am not sure what you 
mean by "QM," but the total charge of the system calculated by either 
DFT, or with Hartree-Fock, is _imposed_ and is not the result of 
calculations -- this sets up the sanity check for the density 
distribution. If you set up your QM calculations by demanding that the 
total charge is zero and the result is nonzero, you probably screwed 
something up with boundaries, basis sets, spin multiplicity, etc, etc, 
so the result is not trustworthy. Obtaining MD parameters from quantum 
chemistry is a whole field in itself.

Alex


On 6/1/2018 12:49 AM, rose rahmani wrote:
> Hi,
>
> I used QM for calculating atoms partial charges for ZnS nanotube but it has
> totally -0.04 charge. I want to study the interaction of this nanotube with
> some biomolecules by AMBER99SB force field.
> Is it wrong to calculate these interaction in presence of -0.04 charge by
> this force field? Should i neglect it?
> Would you please help me or give me a suggestion?
>
> Best regards