[gmx-users] Topology for ligand covalently attached to DNA molecule
sridhar at www.cdfd.org.in
Fri May 23 07:32:01 CEST 2003
I want to simulate a 15 base-pair DNA molecule with a
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.
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