Explicit_Ion_Chromatin

Lammps Implementation of the Explicit-ion Residue-resolution Chromatin Model

Update in 2024

We provide an example src folder of the Lammps 2016 version which include all the customized codes.

Installation guidance

These codes have been tested to run correctly on the Lammps 2016 version.

Copy the codes in "Code/USER-SMOG" to the Lammps src/ folder, then compile for the executables.

Example

• Change the path of the path of relevant environmental variables to the corresponding ones on your computer.

• Running an explicit-ion simulation with a protein-DNA complex structure (PDB code: 1APL).

• Step 1 Prepare the DNA sequence

• Go to the folder protein_DNA/setup/buildDna/ and use the command:

bash genConf.sh

• Step 2 Prepare the structure-based protein model based on the structure
• Go to the folder protein_DNA/setup/sbm_scripts/protein/smog2/ and use the command:

bash cmd.smog2.sh protein.pdb
cd ../
python gen_lmps_file.py

• Step 3 Prepare the protein-DNA complex input file for Lammps;
• Go to the folder protein_DNA/setup/post_processing and use the command:

bash build_one_nucl.sh

• Step 4 Prepare the explicit-ion input file
• Copy the data.prot_dna to the folder protein_DNA/setup/post_processing/add_explicit_ions_100mM_NaCl_200box and execute the command in the folder:

bash cmd.add_ions.sh 

The user needs to have a good estimate of the number of ions based on the targeted ionic concentration.

• Running an explicit-ion simulation with a nucleosome structure (PDB code: 1APL).

• The step is the same as the one used for running the protein-DNA complex structure, except for two additional steps

• Step 2.1 When preparing the protein input file, we need to delete the bonded interactions for the histone tails

• Execute this command in the folder single_nucleosome/setup/sbm_scripts/single_nucl/

bash cmd.remove_idr.sh

• Step 3.1 When preparing the Lammps input file for the nucleosome, we need to run this script in the folder single_nucleosome/setup/post_processing/groupsDefinition/ to generate the file for those domains applying the rigid-body approximation:

python prep_nucl_rigid.py

The user need to determine the number of rigid DNA base pairs by changing the parameters in the file prep_nucl_rigid.py

Reference:

• Xingcheng Lin and Bin Zhang, Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization, eLife (2023), https://doi.org/10.7554/eLife.90073