Script

Topologie related:

Create topologie

Create the topologie file from a structure pdb file

usage: create_top.py [-h] -f F -o O [-vsite]

Named Arguments

-f	Input PDB file
-o	Output directory
-vsite	Use virtual site for hydrogens

Solvate a system

Solvate a gromacs system with water and add ions to neutralize the system charge and to reach an ionic concentration

usage: solvate_ions.py [-h] -f F -p P -o O -n NAME [-d DIST] [-C CONC]

Named Arguments

-f	Input PDB file
-p	Topologie in gromacs format .top
-o	Output Directory
-n	Output file name
-d	Distance between the solute and the box
-C	Ion concentration (mM), default = 0.15 (150mM)

Simulation:

Energy minimization

Minimize a pdb structure in 2 steps, the first step without bonds constraints and the second step with

usage: minimize_pdb.py [-h] -f F -p P -o O -n NAME [-m_steps MIN_STEPS]
                       [-box BOX] [-nt NT] [-ntmpi NTMPI] [-gpu_id GPUID]

Named Arguments

-f	Input PDB file
-p	Topologie in gromacs format .top
-o	Output Directory
-n	Output file name
-m_steps	Minimisation nsteps, default=1000
-box	Create a box, default=False
-nt	Total number of threads to start, default=0
-ntmpi	Number of thread-MPI threads to start, default=0
-gpu_id	List of GPU device id-s to use, default=”“

Equilibration

Equilibrate in 3 steps a system (coor+top), (i) first equilibration with heavy atoms position restraints, (ii) second equilibration with alpha carbon position restraints and (iii) finaly equilibration with weak alpha carbon position restraints

usage: equi_3_step.py [-h] -f F -p P -o O -n NAME [-HA_time HA_TIME]
                      [-CA_time CA_TIME] [-CA_LOW_time CA_LOW_TIME]
                      [-dt_HA DT_HA] [-dt DT] [-nt NT] [-ntmpi NTMPI]
                      [-gpu_id GPUID]

Named Arguments

-f	Input PDB file
-p	Topologie in gromacs format .top
-o	Output Directory
-n	Output file name
-HA_time	Equilibration with HA constraint time(ns), default = 0.25ns
-CA_time	Equilibration with HA constraint time(ns), default = 1ns
-CA_LOW_time	Equilibration with HA constraint time(ns), default = 5ns
-dt_HA	Equi HA dt, default=0.005 (5 fs)
-dt	Equi CA, CA_LOW, dt, default=0.005 (5 fs)
-nt	Total number of threads to start, default=0
-ntmpi	Number of thread-MPI threads to start, default=0
-gpu_id	List of GPU device id-s to use, default=”“

Production

Simulation production

usage: production.py [-h] -f F -p P -o O -n NAME [-time TIME] [-dt DT]
                     [-nt NT] [-ntmpi NTMPI] [-gpu_id GPUID]

Named Arguments

-f	Input PDB file
-p	Topologie in gromacs format .top
-o	Output Directory
-n	Output file name
-time	Production time, default=10
-dt	Equilibration dt, default=0.005 (5 fs)
-nt	Total number of threads to start, default=0
-ntmpi	Number of thread-MPI threads to start, default=0
-gpu_id	List of GPU device id-s to use, default=”“

Peptide related:

Create peptide

Create a linear peptide structure, do a minimisation and a vacuum equilibration

usage: create_peptide.py [-h] -seq SEQ -o O [-m_steps MIN_STEPS] [-time TIME]

Named Arguments

-seq	Peptide sequence
-o	Output Directory
-m_steps	Minimisation nsteps, default=1000
-time	Vacuum equilibration time(ns), default = 1ns

Minimize cyclic peptide

Minimize a cyclic peptide structure in 2 steps, the first step without bonds constraints and the second step with bonds constraints

usage: minimize_pdb_and_cyclic.py [-h] -f F -n NAME [-dir OUT_DIR]
                                  [-m_steps MIN_STEPS] [-keep] [-cyclic]
                                  [-nt NT] [-ntmpi NTMPI] [-gpu_id GPUID]

Named Arguments

-f	Input PDB file
-n	Output file name
-dir	Output directory for intermediate files
-m_steps	Minimisation nsteps, default=1000
-keep	Flag to keep temporary files (without flag output directory will be delete
-cyclic	Flag to indicate if the peptide/protein is cyclic
-nt	Total number of threads to start, default=0
-ntmpi	Number of thread-MPI threads to start, default=0
-gpu_id	List of GPU device id-s to use, default=”“

Insert n copy of a peptide in a system

Create a peptide strucure, insert it around a protein and do the minimisation, equilibration and production.

usage: sim_pep_prot.py [-h] -seq SEQ -npep NUM_MOL [-Pep_time PEP_TIME] -fsys
                       F_SYS -psys P_SYS -ssys S_SYS -o O -n NAME [-dt DT]
                       [-em_steps EM_STEPS] [-dt_HA DT_HA] [-HA_time HA_TIME]
                       [-CA_time CA_TIME] [-CA_LOW_time CA_LOW_TIME]
                       [-maxwarn MAXWARN] [-PROD_time PROD_TIME] [-nt NT]
                       [-ntmpi NTMPI] [-gpu_id GPUID]

Named Arguments

-seq	Peptide sequence
-npep	Number of molecule to insert
-Pep_time	Peptide vacuum equilibration with no constraint time(ns), default = 1ns
-fsys	Input PDB file of the system
-psys	Topologie in gromacs format .top of the system
-ssys	Input tpr file of the system
-o	Output Directory
-n	Output file name
-dt	Equilibration dt, default=0.005 (5 fs)
-em_steps	Minimisation steps, default = 5000
-dt_HA	Equilibration dt, default=0.005 (5 fs)
-HA_time	Equilibration with HA constraint time(ns), default = 0.25ns
-CA_time	Equilibration with HA constraint time(ns), default = 1ns
-CA_LOW_time	Equilibration with HA constraint time(ns), default = 5ns
-maxwarn	Total number of warnings allowed for the equilibration, default=0
-PROD_time	Production time(ns), default = 100ns
-nt	Total number of threads to start, default=0
-ntmpi	Number of thread-MPI threads to start, default=0
-gpu_id	List of GPU device id-s to use, default=”“

~/Documents/repository/gromacs_py/equi_3_step.py -f 1y0m_water_ions/em/em_1y0m_compact.pdb -p 1y0m_water_ions/top/1y0m_water_ions_water_ion.top -o 1y0m_water_ions/ equi/ -n 1y0m -HA_time 0.1 -CA_time 0.2 -CA_LOW_time 0.4