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Last pushed: a year ago
Short Description
NAFlex ABC Setup docker container. MD Setup pipeline following the steps used in ABC project.
Full Description

Docker container to run the Ascona B-DNA Consortium (ABC) Molecular Dynamics Setup protocol from a DNA sequence. naflex-abc-setup-docker internal workflow is powered by NAFlex web services (see reference below).

The setup process is made with leap program from AMBER package and ff12SB (parmBSC0) or ff14SB (parmBSC1) forcefield, Dang ions parameters and SPC/E Water model.

The steps of the pipeline are:

Add missing atoms
Energetically minimize the system
Solvate structure with a truncated octahedron box, with SCP/E water model
Neutralize the system with K+/Na+ ions
Add an ionic concentration of 150mM of Cl- / K+ / Na+ ions
Randomize ions around the structure using cpptraj from AmberTools package

AVAILABILITY:
NAFlex: http://mmb.irbbarcelona.org/NAFlex/ABC
ABC Consortium: https://bisi.ibcp.fr/ABC/Welcome.html

REFERENCES:

Adam Hospital, Ignacio Faustino, Rosana Collepardo-Guevara, Carlos González, Josep Lluís Gelpí, Modesto Orozco.
NAFlex: A web server for the study of nucleic acid flexibility.
Nucleic Acids Research, 2013, 41(W1), W47-W55. NAR Featured Article June 2013.

Ivani, Ivan, Dans Pablo D., Noy Agnes, Pérez Alberto, Faustino Ignacio, Hospital Adam, Walther Jurgen, Andrio Pau, Goni Ramon, Balaceanu Alexandra, Portella Guillem, Battistini Federica, Gelpí Josep Lluis, González Carlos, Vendruscolo Michele, Laughton Charles A., Harris Sarah A., Case David A., and Orozco Modesto
Parmbsc1: a refined force field for DNA simulations.
Nat Methods, 2016 Jan, Volume 13, Issue 1, p.55-8, (2016)

Pérez, Alberto, Marchán Ivan, Svozil Daniel, Sponer Jiri, Cheatham Thomas E., Laughton Charles A., and Orozco Modesto
Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers.
Biophys J, 2007 Jun 1, Volume 92, Issue 11, p.3817-29, (2007)

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adamhospital

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