[gmx-users] Re: gromacs and autodock

[Joanne Hanna]

Hi

I was wondering whether anyone on the list has experience using gromacs
output (with polar Hs) in autodock, as I am struggling with some kind of
seemingly random file format incompatibility.
I was also wondering whether when using autodock people use the kollman
charges or the gmx ff charges for their macromolecule and for ligands
the charges they have derived for their own topologies or the gasteiger
charges. 
I thought it was possibly best to be self consistent and use the same
charges that I have used for docking as I have and will in MD
simulations.

Sorry its a bit of a waffley question.

Hope someone can help

Jo