[gmx-users] Questions regarding the Vacuum force field and Histidine charges

[Joanne Hanna]

Hi

I have three questions like that I would appreciate some suggestions to:

1. When i use either the GROMOS96 43a1 Forcefield (official distribution) or the GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals) to convert my pdb to *.gro format, although i select the  histidines to have one additional hydrogen atom, the overall charge of the His residues after this is 0. Is this correct and if not how do you specify that the histidines should carry a +1 charge.

2. When i use the vacuum force field to do a simulation in vacuum the overall charge of my protein comes out at 0 (from -16) how are these charges counter balanced, and if i am wanting to do a simulation with my ligands Mg2+ and AMP (for which i have created a topology and allocated charges from a gaussian calculation) how do i deal with the charges and smoothing them to be 0.

and 3. Which force field should I be choosing? the GROMOS96 43a1 Forcefield (official distribution) or the GROMOS96 43a2 Forcefield (development) (improved alkane dihedrals)?

Many thanks
Jo
PhD student
University of Warwick