[gmx-users] dna-simualtions with gromacs

[amna khan]

hi .

i want to simulate the DNA in water, all gromacs  force fields does not
support DNA . so i chose the amber force fields from Gromacs package,

i want to ask , are all remaining steps same for DNA simulations like the
lyzome example ?

plase help me

i have done till this step

pdb2gmx -ff amber99sb -f DNAAmber.pdb -o DNA2.pdb -p DNA.top -water spce
-ignh

editconf -bt octahedron -f  DNA2.pdb -o Complex.pdb -d 1.0
genbox -cp Complex.pdb -cs spc216.gro -o Complex_b4ion.pdb -p DNA.top

grompp -f em.mdp -c Complex_b4ion.pdb -p DNA.top -o Complex_b4ion.tpr

genion -s Complex_b4ion.tpr -o Complex_b4em.pdb –nname Na –nn 8 –g
trp_ion.log

rest step can i continue from
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/lysozyme/05_EM.html

please help me i am stuck at this step


regards
amna khan