On 3/23/13 11:19 AM, amna khan wrote:
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
Stuck how? Note that there is no specific procedure that is universally "right"
in terms of equilibration and simulation length. You have to use your best
judgment based on an assessment of the literature and by observing relevant
quantities in your system. Also note that the .mdp files provided in my
tutorial are for OPLS-AA only. The cutoffs and other settings are inappropriate
for AMBER force fields (or any other, for that matter).
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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