acpype使用

acpype -help

usage:
    acpype -i _file_ [-c _string_] [-n _int_] [-m _int_] [-a _string_] [-f] etc. or
    acpype -p _prmtop_ -x _inpcrd_ [-d]


    output: assuming 'root' is the basename of either the top input file,
            the 3-letter residue name or user defined (-b option)
    root_bcc_gaff.mol2:  final mol2 file with 'bcc' charges and 'gaff' atom type
    root_AC.inpcrd    :  coord file for AMBER
    root_AC.prmtop    :  topology and parameter file for AMBER
    root_AC.lib       :  residue library file for AMBER
    root_AC.frcmod    :  modified force field parameters
    root_GMX.gro      :  coord file for GROMACS
    root_GMX.top      :  topology file for GROMACS
    root_GMX.itp      :  molecule unit topology and parameter file for GROMACS
    root_GMX_OPLS.itp :  OPLS/AA mol unit topol & par file for GROMACS (experimental!)
    em.mdp, md.mdp    :  run parameters file for GROMACS
    root_NEW.pdb      :  final pdb file generated by ACPYPE
    root_CNS.top      :  topology file for CNS/XPLOR
    root_CNS.par      :  parameter file for CNS/XPLOR
    root_CNS.inp      :  run parameters file for CNS/XPLOR
    root_CHARMM.rtf   :  topology file for CHARMM
    root_CHARMM.prm   :  parameter file for CHARMM
    root_CHARMM.inp   :  run parameters file for CHARMM


optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        input file name with either extension '.pdb', '.mdl'
                        or '.mol2' (mandatory if -p and -x not set)
  -b BASENAME, --basename BASENAME
                        a basename for the project (folder and output files)
  -x INPCRD, --inpcrd INPCRD
                        amber inpcrd file name (always used with -p)
  -p PRMTOP, --prmtop PRMTOP
                        amber prmtop file name (always used with -x)
  -c {gas,bcc,user}, --charge_method {gas,bcc,user}
                        charge method: gas, bcc (default), user (user's
                        charges in mol2 file)
  -n NET_CHARGE, --net_charge NET_CHARGE
                        net molecular charge (int), for gas default is 0
  -m MULTIPLICITY, --multiplicity MULTIPLICITY
                        multiplicity (2S+1), default is 1
  -a {gaff,amber,gaff2,amber2}, --atom_type {gaff,amber,gaff2,amber2}
                        atom type, can be gaff, gaff2, amber (AMBER14SB) or
                        amber2 (AMBER14SB + GAFF2), default is gaff
  -q {mopac,sqm,divcon}, --qprog {mopac,sqm,divcon}
                        am1-bcc flag, sqm (default), divcon, mopac
  -k KEYWORD, --keyword KEYWORD
                        mopac or sqm keyword, inside quotes
  -f, --force           force topologies recalculation anew
  -d, --debug           for debugging purposes, keep any temporary file
                        created
  -o {all,gmx,cns,charmm}, --outtop {all,gmx,cns,charmm}
                        output topologies: all (default), gmx, cns or charmm
  -z, --gmx4            write RB dihedrals old GMX 4.0
  -t, --cnstop          write CNS topology with allhdg-like parameters
                        (experimental)
  -e {tleap,sleap}, --engine {tleap,sleap}
                        engine: tleap (default) or sleap (not fully matured)
  -s MAX_TIME, --max_time MAX_TIME
                        max time (in sec) tolerance for sqm/mopac, default is
                        10 hours
  -y, --ipython         start iPython interpreter
  -w, --verboseless     print nothing
  -g, --disambiguate    disambiguate lower and uppercase atomtypes in GMX top
                        file
  -u, --direct          for 'amb2gmx' mode, does a direct conversion, for any
                        solvent
  -l, --sorted          sort atoms for GMX ordering
  -j, --chiral          create improper dihedral parameters for chiral atoms
                        in CNS

#默认电荷是bcc，默认力场为gaff

#输入test.pdb文件，输出符号标志符表示为sqm，输出类型为gmx相关
acpype -i test.pdb  -b sqm -o gmx

#输出文件名以及类型如下
em.mdp    md.mdp         sqm_AC.inpcrd  sqm_AC.prmtop      sqm_GMX.gro  sqm_GMX_OPLS.itp  sqm_GMX.top  sqm.mol2  sqm.pdb
leap.log  sqm_AC.frcmod  sqm_AC.lib     sqm_bcc_gaff.mol2  sqm_GMX.itp  sqm_GMX_OPLS.top  sqm.in       sqm.out   sqm.pkl