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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
