求助g_mmpbsa的mutate_traj_tpr.py脚本的使用时输入命令和文件

tianpingpei

g_mmpbsa的mutate_traj_tpr.py脚本可以进行蛋白的残基的突变，此脚本在https://github.com/RashmiKumari/g_mmpbsa下载，我查看了http://rashmikumari.github.io/g_mmpbsa/，此网站上面没有关于这个脚本的介绍，有人用过这个脚本吗？运行这个脚本的命令和输入文件是什么？

puzhongji

usage: mutate_traj_tpr.py [-h] [-drWT wildtype] [-drMT mutations] [-ff 6]
                          [-rr RESIDUE_RANGE] [-rnm ALA] [-nrch] [-hip HIP]
                          [-hid HID] [-glh GLH] [-ash ASH] [-lyn LYN]
                          [-cym CYM] [-emnsteps 10000] [-emct 1.4] [-emtol 10]
                          [-emstep 0.01] [-emnstyp grid] [-t0 0] [-tstep 500]

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

tianpingpei

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