STARTUP COMMAND:
time /schrodinger/macromodel-v90016/bin/IRIX-mips4/ligprep.sh -nt -ac -btc -1 -i 0 -s 1 -isd in.sdf -omae in3D.mae
MMSHARE_EXEC: /schrodinger/mmshare-v14018/bin/IRIX-mips4
STARTUP SCRIPT:
/schrodinger/macromodel-v90016/bin/IRIX-mips4/ligprep_startup
SCHRODINGER: /schrodinger
 
LIGPREP_VERSION 16016
 
JobID:  hyperion-0-437d8a28
--------------------------------
 
Running  ligprep
  input file: in.sdf
  output file: in3D.mae
  # of input structures: 1
Options: 
   -nt -ac -btc -1 -i 0 -s 1 -isd in.sdf -omae in3D.mae
--------------------------------
 
ligprep  running: sdconvert
sdconvert -all -st -isd  in.sdf -omae  in3D_sdout.mae
sdconvert # of output structures: 1
--------------------------------
 
ligprep  running: applyhtreat
applyhtreat in3D_sdout.mae in3D_htout.mae All-atom with No-Lp all 1 
applyhtreat # of output structures: 1
--------------------------------
 
ligprep  running: desalter
desalter in3D_htout.mae in3D_dsout.mae
desalter # of output structures: 1
--------------------------------
 
ligprep  running: stereoizer
stereoizer -n  1 -a in3D_dsout.mae in3D_stout.mae
stereoizer # of output structures: 1
--------------------------------
 
ligprep  running: ring_conf
ring_conf  -l  3  -n  1 in3D_stout.mae in3D_rcout.mae
ring_conf # of output structures: 1
--------------------------------
 
ligprep  running: premin
premin -lic ligprep -m filter -f  10  -s  in3D_prout.mae  -u  in3D_prout_bad.mae in3D_rcout.mae
OK structures in:           in3D_prout.mae
problematic structures in:  in3D_prout_bad.mae
premin # of output structures: 1
premin # of problematic structures: 0
--------------------------------
 
ligprep  running: bmin
/schrodinger/bmin -NO_REDIRECT  in3D_bmrun  >& in3D_bm.log
input file:  in3D_prout.mae
output file:  in3D_bmout.mae
bmin # of output structures: 1
--------------------------------
ligprep  complete
 # of structures in output file ( in3D.mae ): 1
--------------------------------

real	0m9.13s
user	0m3.75s
sys	0m1.67s