Choose the yaml file for cpu only (env.yml) or gpu/cpu (env_gpu.yml) usage.
The env_gpu.yml file can only be installed on a machine with an available GPU.
conda env create --file env.yml
conda activate md
pip install streamd
or the latest version from github
pip install git+https://github.com/ci-lab-cz/streamd.git
-
supports run of multiple simultaneous molecular dynamics simulations
-
supports simulation for different systems:
- Protein in Water;
- Protein - Ligand;
- Protein - Cofactor (multiple);
- Protein - Ligand - Cofactor (multiple);
-
supports of simulations of boron-containing molecules using Gaussian Software
-
supports of simulations of ligand binding metalloproteins with MCPB.py
-
supports distributed computing using dask library
-
supports of running of parallel simulations on multiple servers
-
supports to extend time of MD simulations
-
supports to continue of interrupted MD simulation
-
interrupted MD preparation can be restarted by invoking the same command
-
implemented tools for end-state free energy calculations (gmx_MMPBSA) and Protein-Ligand Interaction analysis (ProLIF)
-
supports customized .mdp files
-
interactive trajectory convergence analysis for multiple complexes
-
GPU support
run_md -h
usage: run_md [-h] [-p FILENAME] [-d WDIR] [-l FILENAME] [--cofactor FILENAME] [--clean_previous_md] [--hostfile FILENAME] [-c INTEGER] [--mdrun_per_node INTEGER]
[--device cpu] [--gpu_ids GPU ID [GPU ID ...]] [--ntmpi_per_gpu int] [--topol topol.top]
[--topol_itp topol_chainA.itp topol_chainB.itp [topol_chainA.itp topol_chainB.itp ...]] [--posre posre.itp [posre.itp ...]]
[--protein_forcefield amber99sb-ildn] [--noignh] [--md_time ns] [--npt_time ps] [--nvt_time ps] [--seed int] [--no_dr] [--not_clean_backup_files]
[--steps [STEPS ...]] [--mdp_dir Path to a directory with specific mdp files] [--wdir_to_continue DIRNAME [DIRNAME ...]] [-o OUT_SUFFIX]
[--deffnm preffix for md files] [--tpr FILENAME] [--cpt FILENAME] [--xtc FILENAME] [--ligand_list_file all_ligand_resid.txt] [--ligand_id UNL]
[--activate_gaussian module load Gaussian/09-d01] [--gaussian_exe g09 or /apps/all/Gaussian/09-d01/g09/g09] [--gaussian_basis B3LYP/6-31G*]
[--gaussian_memory 120GB] [--metal_resnames [MN ...]] [--metal_cutoff 2.8] [--metal_charges {MN:2, ZN:2, CA:2}]
Run or continue MD simulation. Allowed systems: Protein, Protein-Ligand, Protein-Cofactors(multiple), Protein-Ligand-Cofactors(multiple)
options:
-h, --help show this help message and exit
-o OUT_SUFFIX, --out_suffix OUT_SUFFIX
Suffix for output files
Standard Molecular Dynamics Simulation Run:
-p FILENAME, --protein FILENAME
Input file of protein. Supported formats: *.pdb or gro
-d WDIR, --wdir WDIR Working directory. If not set the current directory will be used.
-l FILENAME, --ligand FILENAME
Input file with compound(s). Supported formats: *.mol or sdf or mol2
--cofactor FILENAME Input file with compound(s). Supported formats: *.mol or sdf or mol2
--clean_previous_md Remove a production MD simulation directory if it exists to re-initialize production MD setup
--hostfile FILENAME Text file with addresses of nodes of dask SSH cluster. The most typical, it can be passed as $PBS_NODEFILE variable from inside a PBS script.
The first line in this file will be the address of the scheduler running on the standard port 8786. If omitted, calculations will run on a
single machine as usual.
-c INTEGER, --ncpu INTEGER
Number of CPU per server. Use all available cpus by default.
--mdrun_per_node INTEGER
Number of simulations to run per 1 server.In case of multiple simulations per node, the available CPU cores will be split evenly across these
simulations.By default, run only 1 simulation per node and use all available cpus
--device cpu Calculate bonded and non-bonded interactions on: auto, cpu, gpu
--gpu_ids GPU ID [GPU ID ...]
List of unique GPU device IDs available to use. Use in case of multiple GPUs usage or using exact GPU devices.
--ntmpi_per_gpu int The number of thread-MPI ranks to start per GPU. The default, 1, will start one rank per GPU
--topol topol.top Topology file (required if a gro-file is provided for the protein).All output files obtained from gmx2pdb should preserve the original names
--topol_itp topol_chainA.itp topol_chainB.itp [topol_chainA.itp topol_chainB.itp ...]
itp files for individual protein chains (required if a gro-file is provided for the protein).All output files obtained from gmx2pdb should
preserve the original names
--posre posre.itp [posre.itp ...]
posre file(s) (required if a gro-file is provided for the protein).All output files obtained from gmx2pdb should preserve the original names
--protein_forcefield amber99sb-ildn
Force Field for protein preparation.Available FF can be found at Miniconda3/envs/md/share/gromacs/top
--noignh By default, Streamd uses gmx pdb2gmx -ignh, which re-adds hydrogens using residue names (the correct protonation states must be provided by
user) and ignores the original hydrogens. If the --noignh argument is used, the original hydrogen atoms will be preserved during the
preparation, although there may be problems with recognition of atom names by GROMACS.
--md_time ns Time of MD simulation in ns
--npt_time ps Time of NPT equilibration in ps
--nvt_time ps Time of NVT equilibration in ps
--seed int seed
--no_dr Turn off the acdoctor mode and do not check/diagnose problems in the input ligand file in the next attempt if the regular antechamber run for
ligand preparation fails (ligand_mol2prep.sh script related issues). Use this argument carefully and ensure that you provide valid structures
--not_clean_backup_files
Not to remove all backups of md files
--steps [STEPS ...] Run a particular step(s) of the StreaMD run. Options:1 - run preparation step (protein, ligand, cofactor preparation) 2 - run MD equilibration
step (minimization, NVT, NPT) 3 - run MD simulation 4 - run MD analysis. Ex: 3 4 If 2/3/4 step(s) are used --wdir_to_continue argument should
be used to provide directories with files obtained during the step 1
--mdp_dir Path to a directory with specific mdp files
To use specific MD settings, the user can provide a path to a directory that contains any of the following .mdp files: ions.mdp, minim.mdp,
nvt.mdp, npt.mdp, md.mdp. Missing .mdp files will be replaced by default StreaMD files. Provided .mdp files will be used as templates,
although the system StreaMD parameters (seed, nvt_time, npt_time, md_time, and tc-grps (can not be changed by user)) will override the ones
provided. Warning: The names of the files must be strictly preserved.
--wdir_to_continue DIRNAME [DIRNAME ...]
Single or multiple directories contain simulations created by the tool. Use with steps 2,3,4 to continue run. ' Should consist of: tpr, cpt,
xtc and all_ligand_resid.txt files. File all_ligand_resid.txt is optional and used to run md analysis for the ligands. If you want to continue
your own simulation not created by the tool use --tpr, --cpt, --xtc and --wdir or arguments (--ligand_list_file is optional and required to
run md analysis after simulation )
Continue or Extend Molecular Dynamics Simulation:
--deffnm preffix for md files
Preffix for the md files. Used to run, extend or continue the simulation. If --wdir_to_continue is used files as deffnm.tpr, deffnm.cpt,
deffnm.xtc will be searched from --wdir_to_continue directories
--tpr FILENAME Use explicit tpr arguments to continue a non-StreaMD simulation
--cpt FILENAME Use explicit cpt arguments to continue a non-StreaMD simulation
--xtc FILENAME Use explicit xtc arguments to continue a non-StreaMD simulation
--ligand_list_file all_ligand_resid.txt
If you want automatic md analysis for ligands was run after continue of non-StreaMD simulation you should set ligand_list file. Format of the
file (no headers): user_ligand_id gromacs_ligand_id. Example: my_ligand UNL. Can be set up or placed into --wdir_to_continue directory(ies)
--ligand_id UNL If you want to run an automatic md analysis for the ligand after continue of simulation you can set ligand_id if it is not UNL default value
Boron-containing molecules or MCPBPY usage (use together with Standard Molecular Dynamics Simulation Run arguments group):
--activate_gaussian module load Gaussian/09-d01
String to load gaussian module if necessary
--gaussian_exe g09 or /apps/all/Gaussian/09-d01/g09/g09
Path to gaussian executable or alias. Required to run preparation of boron-containing compounds.
--gaussian_basis B3LYP/6-31G*
Gaussian Basis
--gaussian_memory 120GB
Gaussian Memory Usage
MCPBPY usage (Use together with Standard Molecular Dynamics Simulation Run and Boron-containing molecules arguments group):
--metal_resnames [MN ...]
Metal residue names to run MCPB.py procedure. Start MCPBPY procedure only if gaussian_exe and activate_gaussian arguments are set up,Otherwise
standard gmx2pdb procedure will be run.
--metal_cutoff 2.8 Metal residue cutoff to run MCPB.py procedure
--metal_charges {MN:2, ZN:2, CA:2}
Metal residue charges in dictionary formatStart MCPBPY procedure only if metal_resnames and gaussian_exe and activate_gaussian arguments are
set up, otherwise standard gmx2pdb procedure will be run
Before run MD simulation it is important to prepare protein by yourself to make sure you simulate correct system.
Caution
To prevent problems with recognition of different atom names by Gromacs, we use the -ignh argument, which re-adds the hydrogen atoms, ignoring the original one,
while converting the protein to a gro file (gmx pdb2gmx -water tip3p -ignh). Make sure to rename residues (CYS-CYX, HIS-HIE-HIP) by proper protonation states (more details in Target Preparation section).
As an option, the user can use the --noignh argument when running StreaMD, although there may be problems with atom name recognition that users must resolve themselves or, as another option, provide to Streamd the already prepared protein.gro, topol.top and posre.itp files.
Manual preparation:
- Fill missing residues and loops
Using Chimera:
Tools -> Sequence -> Structure -> Modeller (loops/refinement)
Tools -> Structure Editing -> Dock Prep
-
Explicit water molecules as well as cofactors from a crystal structure can be removed, or if necessarily retained manually;
-
Remove co-crystallizated ligands;
-
Add hydrogens based on protonation states.
- Check states of histidines and put proper aliases HIE, HID or HIP instead of HIS (otherwise protonation can be distorted during MD preparation stage)
type into Chimera cmd:
setattr r type HID :HIS@HD1,DD1,TD1,HND
setattr r type HIP :HID@HE2,DE2,TE2
setattr r type HIE :HIS@HE2
Required to obtain relevant poses of the ligand(s) if needed
- Perform docking procedure
https://github.com/ci-lab-cz/easydock
source activate md
Run simulation for different sytems:
- Protein in Water
run_md -p protein_H_HIS.pdb --md_time 0.1 --nvt_time 100 --npt_time 100 --ncpu 128
- Protein - Ligand
run_md -p protein_H_HIS.pdb -l ligand.mol --md_time 0.1 --nvt_time 100 --npt_time 100 --ncpu 128
- Protein - Cofactor All molecules should present in simulated system, so any problem with preparation of cofactors will interrupt the program.
run_md -p protein_H_HIS.pdb --cofactor cofactors.sdf --md_time 0.1 --nvt_time 100 --npt_time 100 --ncpu 128
To run simulations with boron-containing compounds
Gaussian Software should be available.
Gaussian optimization and charge calculation will be run only for molecules with boron atoms, other molecules will be processed by regular procedure by Antechamber.
If Gaussian cannot be load boron-containing molecules will be skipped.
Any --ligand or --cofactor files can consist of boron-containing compounds
run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 0.1 --npt_time 10 --nvt_time 10 --activate_gaussian "module load Gaussian/09-d01" --gaussian_exe g09 --ncpu 128
To run simulations of Ligand Binding Metalloprotein with MCPB.py
Gaussian Software should be available.
run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 0.1 --npt_time 10 --nvt_time 10 --activate_gaussian "module load Gaussian/09-d01" --gaussian_exe g09 --ncpu 128 --metal_resnames ZN
To run simulations using multiple servers
PBS:
run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 0.1 --npt_time 10 --nvt_time 10 --hostfile $PBS_NODEFILE --ncpu 128
SLURM:
srun hostname | sort | uniq > hostfile
run_md -p protein_H_HIS.pdb -l molecules.sdf --cofactor cofactors.sdf --md_time 0.1 --npt_time 10 --nvt_time 10 --hostfile hostfile --ncpu 128
To continue the interrupted simulations
You can continue the interrupted run by re-executing the previous command. The tool will recognize the checkpoint files and continue the run from the unfinished step.
To extend the simulation
you can continue your simulation unlimited times. As the --md_time argument user should set up the overall time of the simulation
run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_*/ --md_time 0.2
or use explicit --tpr, --cpt and --xtc arguments to continue a non-StreaMD simulation
run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_1/ --md_time 0.3 --tpr protein_H_HIS_ligand_1/md_out.tpr --cpt protein_H_HIS_ligand_1/md_out.cpt --xtc protein_H_HIS_ligand_1/md_out.xtc
in case you don't want to check/run all preparation steps with using non-StreaMD simulations you can use --steps argument
run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_1/ --md_time 0.3 --steps 3 4
Output
each run creates in the working directory (or in the current directory if wdir argument was not set up):
- a unique streaMD log file which name contains name of the protein, ligand file, cofactor file and time of run.
log_protein-fname_ligand-fname_cofactor-fname_start-time.log
Contains important information/warnings/errors about the main program run. - a unique bash log file.
streamd_bash_protein-fname_ligand-fname_cofactor-fname_start-time.log
Contains stdout from Gromacs and Antechamber.
will be created the next folders:
md_files/
- md_preparation/
-- protein/
-- ligands/
-- cofactors/
- md_run/
-- protein-id_ligand-id
md_files/md_preparation/protein/:
protein.gro posre.itp topol.top
OR for multiple chain protein:
md_files/md_preparation/protein/:
protein.gro
topol.top
posre_Protein_chain_A.itp
posre_Protein_chain_B.itp
topol_Protein_chain_A.itp
topol_Protein_chain_B.itp
md_files/md_preparation/ligands/:
all_resid.txt
ligand_1/
ligand_1.frcmod ligand_1.lib ligand_1.top sqm.in
ligand_1.gro ligand_1.mol leap.log sqm.out
ligand_1.inpcrd ligand_1.mol2 posre_ligand_1.itp sqm.pdb
ligand_1.itp ligand_1.prmtop resid.txt tleap.in
ligand_2/
..
md_files/md_preparation/cofactors/:
all_resid.txt
cofactor_1/
cofactor_1.frcmod cofactor_1.lib cofactor_1.top sqm.in
cofactor_1.gro cofactor_1.mol leap.log sqm.out
cofactor_1.inpcrd cofactor_1.mol2 posre_cofactor_1.itp sqm.pdb
cofactor_1.itp cofactor_1.prmtop resid.txt tleap.in
cofactor_2/
md_files/md_run/
protein_H_HIS_ligand_1/
ligand_1.itp density.xvg em.trr ions.tpr md_out.edr md_out.tpr npt.cpt npt.tpr nvt.log potential.xvg rmsd.xvg temperature.xvg
cofactor_1.itp em.edr frame.pdb md_centermolsnoPBC.xtc md_out.gro md_out.xtc npt.edr npt.trr nvt.mdp pressure.xvg rmsf.pdb topol.top
all.itp em.gro gyrate.xvg md_fit.xtc md_out.log md_short_forcheck.xtc npt.gro nvt.cpt nvt.tpr rmsd_cofactor_1.xvg rmsf.xvg
all_ligand_resid.txt em.log index.ndx md.mdp mdout.mdp minim.mdp npt.log nvt.edr nvt.trr rmsd_ligand_1.xvg solv.gro
complex.gro em.tpr ions.mdp md_out.cpt md_out_noj_noPBC.xtc newbox.gro npt.mdp nvt.gro posre.itp rmsd_xtal.xvg solv_ions.gro
protein_H_HIS_ligand_2/
- MD output files
md_fit.xtc - MD trajectory with removed PBC and fitted into Protein or Protein-Ligand group
md_short_forcheck.xtc - short trajectory to check if simulation was valid
frame.pdb - a frame for topology
- Analysis data
potential.png
temperature.png
pressure.png
density.png
rmsd.png - rmsd of the protein against minimized structure
rmsd_xtal.png - rmsd of the protein against crystal structure
rmsd_cofactor_1.png - rmsd of cofactor against minimized structure
rmsd_cofactor_1_xtal.png - rmsd of the ligand against crystal structure
rmsd_ligand_1.png - rmsd of the ligand against minimized structure
rmsd_ligand_1_xtal.png - rmsd of the ligand against crystal structure
rmsf.png - root mean square fluctuation (RMSF, i.e. standard deviation) of atomic positions in the trajectory
gyrate.png - radius of gyration
When run with --device gpu argument the StreaMD offloads nb, update, pme, bonded, pmefft (all which can be run on GPU) computations to GPU.
More details on: https://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html
The performance and gpu usage strongly depend on the type of hardware and size of the system.
It is always good to check the GPU usage (for example, by nvidia-smi command).
Run on 1 GPU:
run_md -p protein_HIS.pdb -l ligand.mol --md_time 1 --device gpu
To improve the performance one can use multiple GPUs or start multiple ranks per GPU.
Run each simulation on multiple GPUs
Warning
Increasing the number of GPUs does not always improve performance. The each single simulation will use all provided GPUs.
run_md -p protein_HIS.pdb -l ligand.mol --md_time 1 --device gpu --gpu_ids 0 1 2 3
Warning
If you want to split the simulations across multiple GPUs but still run the task on the same node use the --mdrun_per_node argument (see below).
Increase the number of thread-MPI ranks per GPU
-ntmpi_per_gpu_ argument is used to calculate total number of thread-MPI ranks (gmx mdrun -ntmpi_ X, where X=ntmpi_per_gpu*number of GPUs to use). By default, ntmpi_per_gpu equals 1, although usage of 2 thread-MPI ranks per GPU may return better performance.
run_md -p protein_HIS.pdb -l ligand.mol --md_time 1 --device gpu -ntmpi_per_gpu 2
Sometimes for more full GPU usage user can start multiple runs on a single/multiple GPU(s) and the tool automatically splits the available CPU cores across these simulations:
run_md -p protein_HIS.pdb -l ligands.sdf --md_time 1 --device gpu --mdrun_per_node 2
To split the simulations across multiple GPUs but still run the task on the same node:
Warning
Although all simulations will still be utilizing all provided GPUs which can lead to suboptimal GPU load. This feature is still under development.
run_md -p protein_HIS.pdb -l ligands.sdf --md_time 1 --device gpu --mdrun_per_node 2 --gpu_ids 0 1
To run mdrun only on CPUs on server where GPUs are available:
run_md -p protein_HIS.pdb -l ligand.mol --md_time 1 --device cpu
To let GROMACS automatically offload calculations on CPU/GPU may be optimal on hardware where the CPUs are relatively powerful compared to the GPUs.
run_md -p protein_HIS.pdb -l ligand.mol --md_time 1 --device auto --gpu_ids 0
The tool is based on gmx_MMPBSA
Calculation arguments can be changed/added by customized mmpbsa.in file
Note
The user can control the length of the trajectory for analysis by editing the startframe, endframe, and interval arguments (in mmpbsa.in file), where every 100 frames equals 1 ns.
run_gbsa -h
usage: run_gbsa [-h] [-i DIRNAME [DIRNAME ...]] [--topol topol.top] [--tpr md_out.tpr] [--xtc md_fit.xtc] [--index index.ndx] [-m mmpbsa.in] [-d WDIR]
[--out_files OUT_FILES [OUT_FILES ...]] [--hostfile FILENAME] [-c INTEGER] [--ligand_id UNL] [-a [STRING ...]] [--clean_previous]
Run MM-GBSA/MM-PBSA calculation using gmx_MMPBSA tool
options:
-h, --help show this help message and exit
-i DIRNAME [DIRNAME ...], --wdir_to_run DIRNAME [DIRNAME ...]
single or multiple directories for simulations. Should consist of: tpr, xtc, ndx files
--topol topol.top topol file from the the MD simulation. Will be ignored if --wdir_to_run is used
--tpr md_out.tpr tpr file from the the MD simulation. Will be ignored if --wdir_to_run is used
--xtc md_fit.xtc xtc file of the simulation. Trajectory should have no PBC and be fitted on the Protein_Ligand group. Will be ignored if --wdir_to_run is used
--index index.ndx Gromacs index file from the simulation. Will be ignored if --wdir_to_run is used
-m mmpbsa.in, --mmpbsa mmpbsa.in
MMPBSA input file. If not set up default template will be used.
-d WDIR, --wdir WDIR Working directory for program output. If not set the current directory will be used.
--out_files OUT_FILES [OUT_FILES ...]
gmxMMPBSA out files (FINAL*.dat) to parse. If set will be used over other variables.
--hostfile FILENAME text file with addresses of nodes of dask SSH cluster. The most typical, it can be passed as $PBS_NODEFILE variable from inside a PBS script.
The first line in this file will be the address of the scheduler running on the standard port 8786. If omitted, calculations will run on a
single machine as usual.
-c INTEGER, --ncpu INTEGER
number of CPU per server. Use all cpus by default.
--ligand_id UNL Ligand residue ID
-a [STRING ...], --append_protein_selection [STRING ...]
residue IDs whuch will be included in the protein system (cofactors).Example: ZN MG
--clean_previous Clean previous temporary gmxMMPBSA files
-o string, --out_suffix string
Suffix for output files
run_gbsa --wdir_to_run md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2 -c 128 -m mmpbsa.in
Output
each run creates in the working directory (or in the current directory if wdir argument was not set up):
- a unique streaMD log file
log_mmpbsa_start-time.log Contains important information/warnings/errors about the main run_gbsa program run. - a unique bash log file.
log_mmpbsa_bash_start-time.log
Contains stdout from gmx_MMPBSA - GBSA_output_start-time.csv with summary csv if MMGBSA method was run
- PBSA_output_start-time.csv with summary csv if MMPBSA method was run
each wdir_to_run has FINAL_RESULTS_MMPBSA_start-time.csv with GBSA/PBSA output.
run_prolif -h
usage: run_prolif [-h] [-i DIRNAME [DIRNAME ...]] [--xtc FILENAME] [--tpr FILENAME] [-l STRING] [-s INTEGER] [-a STRING] [-d WDIR] [-v] [--hostfile FILENAME]
[-c INTEGER] [--width FILENAME] [--height FILENAME] [-o FILENAME] [--not_save_pics]
Get protein-ligand interactions from MD trajectories using ProLIF module.
options:
-h, --help show this help message and exit
-i DIRNAME [DIRNAME ...], --wdir_to_run DIRNAME [DIRNAME ...]
single or multiple directories for simulations.
Should consist of: md_out.tpr and md_fit.xtc files (default: None)
--xtc FILENAME input trajectory file (XTC). Will be ignored if --wdir_to_run is used (default: None)
--tpr FILENAME input topology file (TPR). Will be ignored if --wdir_to_run is used (default: None)
-l STRING, --ligand STRING
residue name of a ligand in the input trajectory. (default: UNL)
-s INTEGER, --step INTEGER
step to take every n-th frame. ps (default: 1)
-a STRING, --append_protein_selection STRING
the string which will be concatenated to the protein selection atoms. Example: "resname ZN or resname MG". (default: None)
-d WDIR, --wdir WDIR Working directory for program output. If not set the current directory will be used. (default: None)
-v, --verbose print progress. (default: False)
--hostfile FILENAME text file with addresses of nodes of dask SSH cluster. The most typical, it can be passed as $PBS_NODEFILE variable from inside a PBS script. The first line in this file will be the address of the scheduler running on the standard port 8786. If omitted, calculations will run on a single machine as usual. (default: None)
-c INTEGER, --ncpu INTEGER
number of CPU per server. Use all cpus by default. (default: 32)
--width FILENAME width of the output pictures (default: 15)
--height FILENAME height of the output pictures (default: 10)
-o FILENAME, --occupancy FILENAME
occupancy of the unique contacts to show (default: 0.6)
--not_save_pics not create html and png files (by frames) for each unique trajectory. Only overall prolif png file will be created. (default: False)
run_prolif --wdir_to_run md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2 -c 128 -v -s 5
Output
- in each directory where xtc file is located plifs.csv, plifs.png,plifs_map.png, plifs.html file for each simulation will be created
- prolif_output_start-time.csv/png - aggregated csv/png output file for all analyzed simulations
To identify converged segments of molecular dynamics trajectories run_analysis module calculates the average root-mean-square deviation (RMSD) of the ligand, protein, and active site residues within 5Å of the ligand, as well as the standard deviation of RMSD for the same trajectory segment. The average RMSD should provide an insight into the ligand movement or rotation relative to its initial pose, while the standard deviation reflects the stability of the ligand pose within the selected trajectory segment. The conclusions can be valuable for subsequent MM-GBSA/PBSA calculations.
usage: run_analysis.py [-h] [-i FILENAME [FILENAME ...]] [--rmsd_type backbone [backbone ...]] [--time_ranges 0-1 5-10 9-10 [0-1 5-10 9-10 ...]] [-d dirname]
[--paint_by PAINT_BY] [-o OUT_SUFFIX] [--title RMSD Mean vs RMSD Std]
Run rmsd analysis for StreaMD output files
options:
-h, --help show this help message and exit
-i FILENAME [FILENAME ...], --input FILENAME [FILENAME ...]
input file(s) with rmsd. Supported formats: *.csv. Required columns: time(ns) ligand_name system. Sep: /\t.
--rmsd_type backbone [backbone ligand ActiveSite]
Column names in the input file to use for the analysis
--time_ranges 0-1 5-10 9-10 [0-1 5-10 9-10 ...]
Time ranges in nanoseconds. Default: Default: start-end, middle-end, end-1 (in nanoseconds)
-d dirname, --wdir dirname
Output files directory
--paint_by csv file File to paint by additional column. Required columns: system, ligand_name. Sep: /\t. The plot will be painted by any other than system and
ligand_name column.
-o OUT_SUFFIX, --out_suffix OUT_SUFFIX
Suffix for output files
--title RMSD Mean vs RMSD Std
Title for html plot. Default: RMSD Mean vs RMSD Std
Such analysis will be performed as a part of the run_md default run or for the separate run the user can use either the --wdir_to_continue directory_path and --steps 4 arguments to perform full analysis of already obtained simulations or the run_analysis script itself (the rmsd file in csv format from run_md will be needed).
preferred way:
run_md --wdir_to_continue md_files/md_run/protein_H_HIS_ligand_1 md_files/md_run/protein_H_HIS_ligand_2 --steps 4 -d md_files
by the script itself:
run_analysis.py -i rmsd_all_systems.csv --rmsd_type "backbone" "ligand" "ActiveSite5.0A" --paint_by exp_data.csv -o protein --title "Protein. RMSD Mean vs RMSD Std" --time_ranges 0-1 0-2 0-10 5-10 9-10
run_prolif applies all this scripts automatically. Use it if you want more detailed analysis or to change the picture/fonts sizes.
prolif_drawmap
Draw prolif plot for analysis binding mode of multiple ligands
prolif_drawmap -h
usage: prolif_drawmap [-h] -i FILENAME [FILENAME ...] [-o FILENAME] [--width FILENAME] [--height FILENAME] [--base_size FILENAME]
Draw prolif plot for analysis binding mode of multiple ligands
options:
-h, --help show this help message and exit
-i FILENAME [FILENAME ...], --input FILENAME [FILENAME ...]
input file with prolif output for the set of molecules. Supported formats: *.csv
Ex: prolif_output.csv
--occupancy float
minimum occupancy of the unique contacts to show
--width int width of the output picture
--height int height of the output picture
--base_size int base size of the output picture
prolif_draw_by_frame
prolif_draw_by_frame -h
usage: prolif_draw_by_frame [-h] -i [FILENAME ...] [-o FILENAME] [--filt_only_H] [--width FILENAME] [--height FILENAME] [--base_size FILENAME]
options:
-h, --help show this help message and exit
-i [FILENAME ...], --input [FILENAME ...]
input file with prolif output for the unique molecule. Supported formats: *.csv
Ex: plifs.csv
--occupancy float
minimum occupancy of the unique contacts to show. Show all contacts by default.
--filt_only_H filt residues where only hydrophobic contacts occur
--width int width of the output picture
--height int height of the output picture
--base_size int base size of the output picture
all system info or errors are saved into logging files which would be placed into your main working directory (the current working directory or the path which was passed through --wdir argument):
run_md:
log_protein-fname_ligand-fname_cofactor-fname_current-date.log - StreaMD logging user info (status of the )
streamd_bash_protein-fname_ligand-fname_cofactor-fname_start-time.log - StreaMD bash system logging info
run_gbsa:
log_mmpbsa_start-time.log - StreaMD logging user info
log_mmpbsa_bash_start-time.log - StreaMD bash system logging info
run_prolif:
log_prolif_start-time.log - StreaMD logging user info
MIT
Ivanova A, Mokshyna O, Polishchuk P.
StreaMD: the toolkit for high-throughput molecular dynamics simulations. ChemRxiv. 2024
https://dx.doi.org/10.26434/chemrxiv-2024-2rjqz