Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Galaxy

Galaxy workflow example that illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI). This workflow returns a resulting protein structure and simulated 3D trajectories.

Designed for running on the https://dev.usegalaxy.es Galaxy instance.

Steps

ID	Name	Description
0	step1_pdb	Download a protein structure from the PDB database biobb_io_pdb_ext
1	step2_fixsidechain	Fix the side chains, adding any side chain atoms missing in the original structure biobb_model_fix_side_chain_ext
2	step3_pdb2gmx	Create Protein System Topology biobb_md_pdb2gmx_ext
3	step4_editconf	Create Solvent Box biobb_md_editconf_ext
4	step5_solvate	Fill the box with water molecules biobb_md_solvate_ext
5	step6_grompp_genion	Add Ions - part 1 biobb_md_grompp_ext
6	step7_genion	Add Ions - part 2 biobb_md_genion_ext
7	step8_grompp_min	Energetically minimize the system - part 1 biobb_md_grompp_ext
8	step9_mdrun_min	Energetically minimize the system - part 2 biobb_md_mdrun_ext
9	step11_grompp_nvt	Equilibriate the system (NVT) - part 1 biobb_md_grompp_ext
10	step10_energy_min	Energetically minimize the system - part 3 biobb_analysis_gmx_energy_ext
11	step12_mdrun_nvt	Equilibrate the system (NVT) - part 2 biobb_md_mdrun_ext
12	step14_grompp_npt	Equilibrate the system (NPT) - part 1 biobb_md_grompp_ext
13	step13_energy_nvt	Equilibrate the system (NVT) - part 3 biobb_analysis_gmx_energy_ext
14	step15_mdrun_npt	Equilibrate the system (NPT) - part 2 biobb_md_mdrun_ext
15	step17_grompp_md	Free molecular dynamics simulation - part 1 biobb_md_grompp_ext
16	step16_energy_npt	Equilibrate the system (NPT) - part 3 biobb_analysis_gmx_energy_ext
17	step18_mdrun_md	Free molecular dynamics simulation - part 2 biobb_md_mdrun_ext
18	step19_rmsfirst	Post-processing resulting 3D trajectory - part 1 biobb_analysis_gmx_rms_ext
19	step22_image	Post-processing resulting 3D trajectory - part 4 biobb_analysis_gmx_image_ext
20	step23_dry	Post-processing resulting 3D trajectory - part 5 biobb_analysis_gmx_trjconv_str_ext
21	step20_rmsexp	Post-processing resulting 3D trajectory - part 2 biobb_analysis_gmx_rms_ext
22	step21_rgyr	Post-processing resulting 3D trajectory - part 3 biobb_analysis_gmx_rgyr_ext

Outputs

ID	Name	Description	Type
mypdb.pdb	mypdb.pdb	n/a	File
myfix_side_chain.pdb	myfix_side_chain.pdb	n/a	File
mypdb2gmx.gro	mypdb2gmx.gro	n/a	File
mypdb2gmx.zip	mypdb2gmx.zip	n/a	File
myeditconf.gro	myeditconf.gro	n/a	File
mysolvate.zip	mysolvate.zip	n/a	File
mysolvate.gro	mysolvate.gro	n/a	File
mygrompp.tpr	mygrompp.tpr	n/a	File
mygenion.gro	mygenion.gro	n/a	File
mygenion.zip	mygenion.zip	n/a	File
_anonymous_output_1	_anonymous_output_1	n/a	File
mymdrun.edr	mymdrun.edr	n/a	File
mymdrun.log	mymdrun.log	n/a	File
mymdrun.xtc	mymdrun.xtc	n/a	File
mymdrun.cpt	mymdrun.cpt	n/a	File
mymdrun.xvg	mymdrun.xvg	n/a	File
mymdrun.trr	mymdrun.trr	n/a	File
mymdrun.gro	mymdrun.gro	n/a	File
_anonymous_output_2	_anonymous_output_2	n/a	File
energy_min.xvg	energy_min.xvg	n/a	File
_anonymous_output_3	_anonymous_output_3	n/a	File
_anonymous_output_4	_anonymous_output_4	n/a	File
_anonymous_output_5	_anonymous_output_5	n/a	File
_anonymous_output_6	_anonymous_output_6	n/a	File
_anonymous_output_7	_anonymous_output_7	n/a	File
_anonymous_output_8	_anonymous_output_8	n/a	File
_anonymous_output_9	_anonymous_output_9	n/a	File
_anonymous_output_10	_anonymous_output_10	n/a	File
energy_nvt.xvg	energy_nvt.xvg	n/a	File
_anonymous_output_11	_anonymous_output_11	n/a	File
_anonymous_output_12	_anonymous_output_12	n/a	File
_anonymous_output_13	_anonymous_output_13	n/a	File
_anonymous_output_14	_anonymous_output_14	n/a	File
_anonymous_output_15	_anonymous_output_15	n/a	File
_anonymous_output_16	_anonymous_output_16	n/a	File
_anonymous_output_17	_anonymous_output_17	n/a	File
_anonymous_output_18	_anonymous_output_18	n/a	File
energy_npt.xvg	energy_npt.xvg	n/a	File
_anonymous_output_19	_anonymous_output_19	n/a	File
_anonymous_output_20	_anonymous_output_20	n/a	File
_anonymous_output_21	_anonymous_output_21	n/a	File
_anonymous_output_22	_anonymous_output_22	n/a	File
_anonymous_output_23	_anonymous_output_23	n/a	File
_anonymous_output_24	_anonymous_output_24	n/a	File
_anonymous_output_25	_anonymous_output_25	n/a	File
rmsd_first.xvg	rmsd_first.xvg	n/a	File
mygmx_image.xtc	mygmx_image.xtc	n/a	File
mygmx_trjconv_str.xtc	mygmx_trjconv_str.xtc	n/a	File
rmsd_exp.xvg	rmsd_exp.xvg	n/a	File
mygmx_rgyr.xvg	mygmx_rgyr.xvg	n/a	File

Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Galaxy
Version 1

Steps

Outputs

Version History

Version 1 (earliest) Created 26th Sep 2021 at 20:50 by Douglas Lowe

Creators

Submitter

Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Galaxy Version 1

Steps

Outputs

Version History

Version 1 (earliest) Created 26th Sep 2021 at 20:50 by Douglas Lowe

Creators

Submitter

Related items

Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Galaxy
Version 1