[gmx-users] Topology for ligand covalently attached to DNA molecule

[Mr.Sridhar]

Hi gmxusers,

I want to simulate a 15 base-pair DNA molecule with a
"pyrrolo-benzo-di-azamine" (PBD)
ligand covalently attached to one of the N of one of the quanine bases.
How to build the topology for the whole system ?

If I include the topology obtained from PRODRG server for PBD seperately,
will the covalent link between  DNA and PBD be taken into consideration ?

else what is the procedure to be followed ?

What is the forcefield that is best for simulations involving DNA/RNA ?

Thanking you in anticipation of your suggessions.

sridhar.