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