[gmx-users] Question about ffamber in Gromacs

[bo yang]

Dear gromacs user,

I am doing the MD simulation of CNT-DNA interaction.
Before introducing DNA, I used gromacs default force field
and finished the simulation of CNT (carbon nanotube). And,
in the ffgmxnb.itp, I introduced the non-bonded parameters
for C-C and C-OW (oxygen) in the [non-bonded param] session.

Now, I have the amber99 package. I opened ffamber99nb.itp and
compared the format of ffamber99nb.itp to ffgmxnb.itp.
There is only [atoms] session in ffamber99nb.itp.

Do you mind telling me how to introduce these non-bonded
parameters (L-J parameters) for C-C and C-OW in ffamber?
Do I just simply add [non-bonded param] at the end of the ffamber99nb.itp
and list the parameters there?

I guess this is important for me because I attempted to add [non-bonded
param]
at the end of the itp file. After the energy minimization, I visualized that
the
carbon nanotube is standing above the simulation box.

Also, I realize that the atom mass in ffamberXX.itp is 0, but in
ffamberXX.atp,
all masses are non-zero.  Do you minding explain it for me in detail?

I appreciate your help.

Regards!
Bo
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