do you have all-atom DNA data file?

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1

Hi sir

Now I am trying to simulate the process of coarse-grained DNA translocating through graphene nanopores, I need to find out the pair potential parameters. I need the all-atom DNA information which is needed in the data file that LAMMPS can read by command read_data, including masses, bonds, angles, dihedrals and atoms coordinates. Could you please give me a file if you have it. Thanks very much.

Best regards

Rita Zhou

2

Oh dear. I'll do my best to attempt an answer.

Unlike some other popular MD programs which are specialised for this
task, LAMMPS does not come with software to build, solvate, and prep
all-atom biomolecules. (Honestly, I never thought it was that easy to
do, even with the right software.)

Hopefully I can point you to some relevant web pages. (If I misspoke,
or I omitted something, I hope somebody will correct me.)

There are many steps required:

-- outline --
1) Coordinates are (unfortunately still) usually stored in PDB format.
You need to obtain a PDB file containing the DNA molecule you want to
simulate (see below).

2) Solvate the molecule. (I assume you want to simulate it in
explicit solvent. If not, you are out of luck. LAMMPS does not yet
support GBSA-based implicit solvent.)

3) Use the coordinates from the PDB file you created (including DNA
and water), and combine them with topology and force-field parameters
(for example from a file like leaprc.ff99, and TIP3P, or some similar
file), to construct a LAMMPS DATA file.

3

Setting up and running DNA simulations requires some care. DNA molecules are highly charged and alreade neutralizing incorrectly can lead to problems. Rather than using some random file from some random person you don't know anything about, I would recommend to officially collaborate with a group that has the proper expertise.

If you don't want to collaborate, then you need to get the necessary experience yourself using software like charmm or namd or amber or gromacs that has the necessary tools to build such systems and the topology files.

Remember: there aint no escape from the blues.
Axel