[gmx-users] problem with genion

[Youkun Gao]

hi everyone,
i have two problems,
first, i want to find out, if there is any interaction between two alpha
helices. i cut of a helix from a pdb file and then duplicate this one, put
them together (some residues have distance about ca. 3 A, corresponding the
hydrogen bond distance) then i use steep to minimize the energy, following
with cg, and after that i enlarged the box size, filled with SPC water, when i
changed some water into Na and Cl, it gave the information, "killed", although
i did nothing? what was the problem?
second, the protein, which i download from data base, has GTP molecule, is
this molecule in gromacs also defined? how can i use pdb2gmx to make a itp
file?
thanks a lot
Gao