ABC DNA MD Setup (AMBER)

Ascona B-DNA Consortium MD setup for a DNA duplex with AmberTools: parmbsc1 topology, OPC water box, salt, hydrogen mass repartitioning, 10-step equilibration and free MD.

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Ascona B-DNA Consortium MD setup for a DNA duplex with AmberTools: parmbsc1 topology, OPC water box, salt, hydrogen mass repartitioning, 10-step equilibration and free MD.

Domain: BioExcel Building Blocks

Overview

Ascona B-DNA Consortium (ABC) MD setup for the Drew-Dickerson dodecamer (CGCGAATTCGCG) with AmberTools. It builds a parmbsc1 DNA topology, solvates it in a truncated octahedron OPC water box, adds KCl (100 mM by default), randomizes ion positions with cpptraj, applies hydrogen-mass repartitioning with parmed for a 4 fs timestep, runs the 10-step Roe & Brooks equilibration with sander, and finishes with a free production MD run. The workflow has 26 tasks.

Pipeline

leap_gen_top               Build DNA topology (parmbsc1, leap)
leap_solvate               Solvate in truncated octahedron box (leap)
leap_add_ions              Neutralize + add salt (leap)
cpptraj_randomize_ions     Randomize ion positions (cpptraj)
parmed_hmassrepartition    Hydrogen-mass repartition for 4 fs (parmed)
sander_eq1..eq10           10 equilibration steps (minimization, heating, NPT)
process_eq1..eq10          Extract energy and pressure/density per step
sander_md                  Free production MD (4 fs)

Inputs / Outputs

Inputs: the parameters below (starting structure and the 11 sander MDIN files ABCix_config_files/step1.in ... step10.in, md.in).

Outputs (results/):

Parameters

| id | Default | Meaning | |---|---|---| | dna_pdb | CGCGAATTCGCG.pdb | Initial DNA duplex structure (PDB). | | positive_ion | K+ | Counter-ion (K+, Na+). | | box_padding_a | 15.0 | Minimum distance in angstrom between the DNA and the box edge (8-25). | | ionic_concentration_mm | 100 | Added salt in mM on top of neutralization (0-1000). | | md_steps | 500 | Production steps at 4 fs (500 = 2 ps; 25,000,000 = 100 ns). | | step1_mdin ... step10_mdin, md_mdin | ABCix_config_files/*.in | sander MDIN files for equilibration and production (expert). |

References