optional arguments:
-h, --help show this help message and exit
-drWT wildtype, --dirWildType wildtype
Directory containing wild-type frames from MD
trajectory
-drMT mutations, --dirMutations mutations
Directory containing mutated frames from MD trajectory
-ff 6, --force_field 6
Force-field number to choose in pdb2gmx. Default value
is 6, which corrosponds to AMBER99SB-ILDN force-field
in standard GROMACS package
-rr RESIDUE_RANGE, --residue_range RESIDUE_RANGE
Input residue range and/or list with respective chain
for mutating residues to ALA. e.g. -rr
'A:27,45,67-70;B:40,43,78-80'
-rnm ALA, --residue_name ALA
Target residue name for mutation. e.g. for Alanine
scanning: -rnm 'ALA'
-nrch, --no_orig_h_pos
Do not recover original coordinates of hydrogen atoms.
-hip HIP, --hip HIP HIS residues need to be protonated as HIP. Usage: e.g.
-hip 'A:23,34,56;B:32,56'
-hid HID, --hid HID HIS residues need to be as HID. Usage: e.g. -hid
'A:23,34,56;B:32,56'
-glh GLH, --glh GLH GLU residues need to be protonated as GLH. Usage: e.g.
-glh 'A:23,34,56;B:32,56'
-ash ASH, --ash ASH ASP residues need to be protonated as ASH. Usage: e.g.
-ash 'A:23,34,56;B:32,56'
-lyn LYN, --lyn LYN LYS residues need to be neutral as LYN. Usage: e.g.
-lyn 'A:23,34,56;B:32,56'
-cym CYM, --cym CYM CYS residues need to be deprotonated as CYM. Usage:
e.g. -cym 'A:23,34,56;B:32,56'
-emnsteps 10000, --em_nsteps 10000
Number of minimization steps (nsteps)
-emct 1.4, --em_cutoff 1.4
Cut-off in nm during energy minimization
-emtol 10, --emtol 10
Tolerance value (emtol) for energy minimization
-emstep 0.01, --emstep 0.01
Minimization step (emstep) for energy minimization
-emnstyp grid, --em_ns_type grid
Cut-off scheme during energy minimization
-t0 0, --time0 0 Starting time (ps) of mutated trajectory
-tstep 500, --timestep 500
Time step (ps) between frames of mutated trajectory 作者Author: tianpingpei 时间: 2019-7-30 11:24
谢谢puzhongji的回复，对比MmPbSaStat.py脚本中就有parser = argparse.ArgumentParser()
parser.add_argument("-mt", "--multiple", help='If given, calculate for multiple complexes. Need Metafile containing path of energy files', action="store_true")
parser.add_argument("-mf", "--metafile", help='Metafile containing path to energy files of each complex in a row obtained from g_mmpbsa in following order: \
[MM file] [Polar file] [ Non-polar file] ',action="store", default='metafile.dat', metavar='metafile.dat')
parser.add_argument("-m", "--molmech", help='Vacuum Molecular Mechanics energy file obtained from g_mmpbsa',action="store", default='energy_MM.xvg', metavar='energy_MM.xvg')
parser.add_argument("-p", "--polar", help='Polar solvation energy file obtained from g_mmpbsa',action="store",default='polar.xvg', metavar='polar.xvg')
parser.add_argument("-a", "--apolar", help='Non-Polar solvation energy file obtained from g_mmpbsa',action="store",default='apolar.xvg',metavar='apolar.xvg')
parser.add_argument("-bs", "--bootstrap", help='If given, Enable Boot Strap analysis',action="store_true")
parser.add_argument("-nbs", "--nbstep", help='Number of boot strap steps for average energy calculation',action="store", type=int, default=500, metavar=500)
parser.add_argument("-of", "--outfr", help='Energy File: All energy components frame wise',action="store",default='full_energy.dat', metavar='full_energy.dat')
parser.add_argument("-os", "--outsum", help='Final Energy File: Full Summary of energy components',action="store",default='summary_energy.dat', metavar='summary_energy.dat')
parser.add_argument("-om", "--outmeta", help='Final Energy File for Multiple Complexes: Complex wise final binding nergy',action="store",default='meta_energy.dat',metavar='meta_energy.dat')，我们就可以看出运行MmPbSatat.py脚本的命令是python MmPbSatat.py -m energy_MM.xvg -p polar.xvg -a sasa.xvg,但是在此脚本中没有发现这种提示，因此我无法确定运行此脚本的命令