# You can alter the variables below to change what info is printed out
INPUT['debug_printlevel'] = 0
INPUT['verbose'] = 1
INPUT['csv_format'] = 1
INPUT['dec_verbose'] = 0
#
# MODIFY NOTHING BELOW HERE, OR GET WHAT YOU DESERVE
INPUT['nmode_igb'] = 1
INPUT['solvcut'] = 14.0
INPUT['linit'] = 1000
INPUT['nmendframe'] = 1000000
INPUT['probe'] = 1.4
INPUT['inp'] = 2
INPUT['exdi'] = 80.0
INPUT['dielc'] = 1.0
INPUT['cavity_offset'] = -0.5692
INPUT['receptor_mask'] = ':1-27'
INPUT['saltcon'] = 0.0
INPUT['entropy'] = 0
INPUT['solvbox'] = '-1,-1,-1'
INPUT['qmcharge_lig'] = 0
INPUT['keep_files'] = 1
INPUT['pbrun'] = True
INPUT['fillratio'] = 4.0
INPUT['gbrun'] = False
INPUT['istrng'] = 0.0
INPUT['ligand_mask'] = ':28-29'
INPUT['qmcharge_rec'] = 0
INPUT['endframe'] = 10
INPUT['mutant_only'] = 0
INPUT['ng'] = '-1,-1,-1'
INPUT['nmstartframe'] = 1
INPUT['igb'] = 5
INPUT['closureorder'] = 1
INPUT['radiopt'] = 0
INPUT['rismrun_std'] = False
INPUT['tolerance'] = 1e-05
INPUT['qmcut'] = 9999.0
INPUT['thermo'] = 'std'
INPUT['qm_theory'] = ''
INPUT['buffer'] = 14.0
INPUT['alarun'] = False
INPUT['print_res'] = 'all'
INPUT['surfoff'] = 0.0
INPUT['search_path'] = 0
INPUT['surften'] = 0.0072
INPUT['molsurf'] = 0
INPUT['qmcharge_com'] = 0
INPUT['drms'] = 0.001
INPUT['scale'] = 0.5
INPUT['grdspc'] = 0.5
INPUT['sander_apbs'] = 0
INPUT['qm_residues'] = ''
INPUT['rismrun_gf'] = False
INPUT['maxcyc'] = 10000
INPUT['netcdf'] = ''
INPUT['nmode_istrng'] = 0.0
INPUT['closure'] = 'kh'
INPUT['use_sander'] = 1
INPUT['nminterval'] = 1
INPUT['ifqnt'] = 0
INPUT['temp'] = 298.15
INPUT['polardecomp'] = 0
INPUT['rism_verbose'] = 0
INPUT['cavity_surften'] = 0.0378
INPUT['interval'] = 1
INPUT['full_traj'] = 0
INPUT['strip_mask'] = ':WAT,Cl-,CIO,Cs+,IB,K+,Li+,MG2,Na+,Rb+'
INPUT['nmoderun'] = False
INPUT['prbrad'] = 1.4
INPUT['msoffset'] = 0.0
INPUT['decomprun'] = False
INPUT['rismrun'] = False
INPUT['startframe'] = 1
INPUT['indi'] = 1.0
INPUT['idecomp'] = 0
FILES.clean = False
FILES.complex_prmtop = 'DNA_AMP_ante.prmtop'
FILES.input_file = 'mmpbsa.in'
FILES.ligand_mdcrd = None
FILES.ligand_prmtop = 'AMP_ante.prmtop'
FILES.make_mdins = False
FILES.mdcrd = ['test.dcd']
FILES.mutant_complex_prmtop = 'mutant_complex_prmtop'
FILES.mutant_ligand_prmtop = None
FILES.mutant_receptor_prmtop = None
FILES.prefix = '_MMPBSA_'
FILES.receptor_mdcrd = None
FILES.receptor_prmtop = 'DNA_ante.prmtop'
FILES.solvated_ligand_prmtop = None
FILES.solvated_prmtop = 'DNA_AMP_wb_vmd.prmtop'
FILES.solvated_receptor_prmtop = None
FILES.use_mdins = False
FILES.xvvfile = '/home/dy/amber12/dat/mmpbsa/spc.xvv'
size = 1
numframes = 10
numframes_nmode = 0
mut_str = 'None'
|Input file:
|--------------------------------------------------------------
|Input file for running PB and GB
|&general
|   use_sander=1, endframe=10, verbose=1,
|#   entropy=1,
|/
|&pb
|
|/
|--------------------------------------------------------------
