[gmx-users] charge group assignment with AMBER parameters

[Jacob Spooner]

I am attempting a simulation of a drug molecule using the ffamber/gaff within gromacs.  When it comes to assigning charge groups the manual says that one should group together nearby atoms and  the groups should have a net integer charge.  Since AMBER charge parameters are obtained from QM calculations of the specific molecule they do not form into integer charge groups like with OPLS whose charge parameters are dictated by atom type and stay the constant in different molecules.  I was wondering if somebody who has worked with AMBER in GROMACS could give some guidance with regards to charge group assignment.  

Thanks

Jake Spooner
University of the Fraser Valley