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Brownian Dynamics simulations of yeast NPC FG repeats

Brownian Dynamics simulations of yeast NPC FG repeats PubMed logo PDB-Dev

tickVerified to work with the latest stable IMP release (2.9.0). The files are also available at GitHub.
Additional software needed to use these files: IMP protobuf install instructions

Anaconda logo To install the software needed to reproduce this system with the Anaconda Python command line tool (conda), run the following commands:

conda config --add channels salilab
conda install imp protobuf

UCSF logo To set up the environment on the UCSF QB3 cluster to run this system, run:

module load imp python/protobuf
Tags Brownian dynamics

DOI

Overview

Synopsis: The files in this folder can be used to reproduce the Brownian Dynamics simulations of FG repeats using IMP as described in Kim et al., 2018

Author: Barak Raveh

E-mail: barak.raveh@gmail.com or barak@salilab.org

Date last updated: Jan 9th, 2018

Main folders

Scripts/ - scripts for generating the FG repeats over an input scaffold

InputData/ - folder of input RMF file describing the scaffold

Output/ - output from running the script, as explained below

SampleOutput/ - sample of the main output from running the script

RepresentativeEnsemble/ - ensemble of output models (extracted from simulation outputs stored on Andrej's Salilab park4 file system, in folder /salilab/park4/barak/Runs/NPC_FullModel2016/FullNPC_Oct10_Cluster0model_Rg70_per_600aa_InflateObstacles_InflatedKaps, see .../Ensemble/make_ensemble.sh there). The accompanying .dcd file contains a larger number of structures from the same ensemble in CHARMM/NAMD DCD format, designed to work together with the NPC mmCIF structure deposited at PDB-Dev. It is generated using util/to_dcd.py.

Densities/ - densities of various nups and all nups, from same folder as RepresentativeEnsemble/

Prerequisites

  1. Download IMP (https://github.com/salilab/imp) - a recent nightly (or develop) build is needed

  2. Build IMP according to online instructions, including the IMP.npctransport module (this requires Protobuf)

Protocol for generating FG repeats from scaffold of NPC

  1. Create folder for output, e.g. "Output"

  2. Create model of NPC from RMF file of scaffold (expected running time - a few minutes) in output folder ("Output" in this example):

    $ Scripts/load_whole_new_coarse_grained_v5.py Output/config.pb InputData/47-35_1spoke.rmf3 >& Output/config.txt &

  3. move to Output folder:

    $ cd Output

  4. Equilibrate and run for as long as desired by changing short_init_factor and short_sim_factor for shorter or longer equilibration and simulation, respectively, and using a specific random seed using optional --random_seed flag; output file and movie file names could be changed as well, use --help option for more information (expected running time - hours to days depending on simulation time and system):

    $ fg_simulation --configuration config.pb --output output.pb --short_init_factor 0.25 --short_sim_factor 1.0 --conformations movie.rmf --random_seed $RANDOM >& LOG.fg_simulation &

  5. The output movie file movie.rmf can be viewed using e.g. Chimera.

Information

Author(s): Barak Raveh

Date: March 8th, 2018

License: CC-BY-SA-4.0. This work is freely available under the terms of the Creative Commons Attribution-ShareAlike 4.0 International License.

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