3 files

Microsecond molecular dynamics simulation of kinase domain of the human tyrosine kinase ABL1

posted on 2016-12-25, 00:57 authored by John ChoderaJohn Chodera, Sonya HansonSonya Hanson
This is a one microsecond trajectory of the catalytic domain of the human tyrosine protein kinase ABL1 (UNIPROT:ABL1_HUMAN, residues 242-493). The simulation was generated on Folding@home using OpenMM 6.3.1 with the AMBER99SB-ILDN forcefield, TIP3P water, and neutralizing salt. A Langevin integrator with 2 fs timestep, 300 K temperature, and 1/ps collision rate was used. PME with a nonbonded cutoff of 1.0 nm was used with default tolerance of 5.0e-4. A long-range isotropic dispersion correction was used to correct for the truncation of Lennard-Jones interactions at 1.0 nm. A molecular-scaling Monte Carlo barostat was applied using a 1 atm reference pressure, with MC moves attempted every 50 steps. Coordinates were saved every 250ps, and waters and ions stripped. The trajectory file contains 4000 snapshots. Initial models were generated with Ensembler (see References) using the ABL1 structure from chain B of PDB ID: 2GQG as a template.

* run17-clone3.jpg - image of initial simulation snapshot
* run17-clone3.pdb - PDB file of initial simulation snapshot
* run17-clone3.h5 - MDTraj HDF5 format trajectory

To convert the trajectory, see the MDTraj `mdconvert` command:

For information on installing MDTraj, see:


The authors acknowledge support from the Sloan Kettering Institute and NIH grant P30 758 CA008748.