numero i dont remember

So, couple of hints on Autodock and Gromacs.

A problem that was haunting me was a constant error "NOTE: all energies are equal in population". the solution is - use Autodock 4.2.

Second problem was the "Warning: attempt to divide by zero" It appears that autodock does not digest the alternative atom coordinates in the PDB's. to solve that delete either of the alt locations and run a small script to fix atom seq id's. Or just take a different PDB file.

Running gromacs is pretty straightforward. the only note is that genion sometimes does a crappy job when you want to replace some specific molecules with ions (selected from index group) so you need to write a small script that will fix the atom and residue ids.

so long.