######## begin of dock-1lzs-A-nowater-XP-0001.log ######### Glide version 87072 (mmshare version 50072) Copyright (c) Schrodinger, LLC. All Rights Reserved. -------------------------------------------------------------------------------- JobId : bambam-0-5f3ffce7 Name : dock-1lzs-A-nowater-XP-0001 Program : Glide Host : bambam.cchem.berkeley.edu Dir : /scr/kathy/dock-1lzs-A-nowater-XP HostEntry : localhost JobHost : bambam.cchem.berkeley.edu JobDir : /scr/kathy/dock-1lzs-A-nowater-XP-0001 JobSchrodinger : /home/mgcf/software-ws/schrodinger2020-2 Commandline : /home/mgcf/software-ws/schrodinger2020-2/glide -RESTART -serial dock-1lzs-A-nowater-XP-0001.inp -HOST localhost StartTime : 2020-08-21-09:57:12 -------------------------------------------------------------------------------- [running at reduced cpu priority] VdW radii of ligand atoms scaled by 0.800000000000000 Charge cutoff for polarity 0.150000000000000 After readscreen, (nx, ny, nz) = ( 32 , 32 , 32 ). Receptor setup: (nsites, nx, ny, nz, bsize)=( 125 , 32 , 32 , 32 , 1.00000000000000 ). Screening setup finished. DOCKMAIN: getting receptor. DOCKMAIN after grid: (nx, ny, nz) = ( 88 , 88 , 88 ). DOCKMAIN: Grid setup finished Calling OPLS3e atomtyping ... Finished parameter assignment Reading torsion control file '/home/mgcf/software-ws/schrodinger2020-2/glide-v8.7/bin/Linux-x86_64/../../data/torcontrol.txt': Using generalized torsion control Number of rotatable bonds 28 Using templates for ring conformations. Glide Extra Precision Mode active. GlideScore version XP5.0 will be used Buried polar penalty 0.000 Coulomb vdW cutoff 0.000 H bond cutoff 0.000 Metal-ligand cutoff 10.000 Assigning GlideScore XP5.0 parameters For Glide Extra Precision mode, will use maxref = 800 res reso default 16.0000000000000 16.0000000000000 res reso fin 16.0000000000000 16.0000000000000 Use grow mode-t res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 REPORT POSE ANCH_2 1 0 6 REPORT POSE ANCH_2 2 0 4 REPORT POSE ANCH_2 3 0 35 REPORT POSE ANCH_2 4 0 28 REPORT POSE ANCH_2 5 0 44 REPORT POSE ANCH_2 6 0 26 REPORT POSE ANCH_2 7 0 38 REPORT POSE ANCH_2 8 0 12 REPORT POSE ANCH_2 9 0 18 REPORT POSE ANCH_2 10 0 30 Full force-field refinement in receptor field for up to 10 poses 10 poses will be postminimized for this ligand iancorig for REPORT pose 1 0 iancorig for REPORT pose 2 0 iancorig for REPORT pose 3 0 iancorig for REPORT pose 4 0 iancorig for REPORT pose 5 0 iancorig for REPORT pose 6 0 iancorig for REPORT pose 7 0 iancorig for REPORT pose 8 0 iancorig for REPORT pose 9 0 iancorig for REPORT pose 10 0 Reporting postminimized pose 1 GlideScore = -11.294 GlideScore( -11.29)+Epik State Penalty( 0.00) = -11.29 kcal/mol DOCKING RESULTS FOR LIGAND 1 (5288898) Best XP pose: 6; GlideScore = -11.29 Emodel = -112.11 E = -75.20 Eint = 13.46 Calling OPLS3e atomtyping ... Finished parameter assignment Number of rotatable bonds 28 Using templates for ring conformations. Glide Extra Precision Mode active. For Glide Extra Precision mode, will use maxref = 800 res reso default 16.0000000000000 16.0000000000000 res reso fin 16.0000000000000 16.0000000000000 Use grow mode-t res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 REPORT POSE ANCH_2 1 0 19 REPORT POSE ANCH_2 2 0 43 REPORT POSE ANCH_2 3 0 39 REPORT POSE ANCH_2 4 0 36 REPORT POSE ANCH_2 5 0 23 REPORT POSE ANCH_2 6 0 9 REPORT POSE ANCH_2 7 0 14 REPORT POSE ANCH_2 8 0 20 REPORT POSE ANCH_2 9 0 42 REPORT POSE ANCH_2 10 0 10 10 poses will be postminimized for this ligand iancorig for REPORT pose 1 0 iancorig for REPORT pose 2 0 iancorig for REPORT pose 3 0 iancorig for REPORT pose 4 0 iancorig for REPORT pose 5 0 iancorig for REPORT pose 6 0 iancorig for REPORT pose 7 0 iancorig for REPORT pose 8 0 iancorig for REPORT pose 9 0 iancorig for REPORT pose 10 0 Reporting postminimized pose 7 GlideScore = -10.415 GlideScore( -10.41)+Epik State Penalty( 0.00) = -10.41 kcal/mol DOCKING RESULTS FOR LIGAND 2 (chitin) Best XP pose: 14; GlideScore = -10.41 Emodel = -111.63 E = -73.84 Eint = 13.60 REPORT OF DOCKED POSES The ligand structures were written to the file dock-1lzs-A-nowater-XP-0001_raw.maegz Exiting Glide Date: Friday, August 21 2020, at 10:30:32 PDT CPU time (s): 1979.5 user, 17.3 system, 1997.1 real Total elapsed time = 1997 seconds (33 minutes, 17 seconds) [running at reduced cpu priority] ######## end of dock-1lzs-A-nowater-XP-0001.log ######### ######## begin of dock-1lzs-A-nowater-XP-0002.log ######### Glide version 87072 (mmshare version 50072) Copyright (c) Schrodinger, LLC. All Rights Reserved. -------------------------------------------------------------------------------- JobId : bambam-0-5f4004c2 Name : dock-1lzs-A-nowater-XP-0002 Program : Glide Host : bambam.cchem.berkeley.edu Dir : /scr/kathy/dock-1lzs-A-nowater-XP HostEntry : localhost JobHost : bambam.cchem.berkeley.edu JobDir : /scr/kathy/dock-1lzs-A-nowater-XP-0002 JobSchrodinger : /home/mgcf/software-ws/schrodinger2020-2 Commandline : /home/mgcf/software-ws/schrodinger2020-2/glide -RESTART -serial dock-1lzs-A-nowater-XP-0002.inp -HOST localhost StartTime : 2020-08-21-10:30:43 -------------------------------------------------------------------------------- [running at reduced cpu priority] Offsetting ligand numbers by 2 VdW radii of ligand atoms scaled by 0.800000000000000 Charge cutoff for polarity 0.150000000000000 After readscreen, (nx, ny, nz) = ( 32 , 32 , 32 ). Receptor setup: (nsites, nx, ny, nz, bsize)=( 125 , 32 , 32 , 32 , 1.00000000000000 ). Screening setup finished. DOCKMAIN: getting receptor. DOCKMAIN after grid: (nx, ny, nz) = ( 88 , 88 , 88 ). DOCKMAIN: Grid setup finished Calling OPLS3e atomtyping ... Finished parameter assignment Reading torsion control file '/home/mgcf/software-ws/schrodinger2020-2/glide-v8.7/bin/Linux-x86_64/../../data/torcontrol.txt': Using generalized torsion control Number of rotatable bonds 24 Using templates for ring conformations. Glide Extra Precision Mode active. GlideScore version XP5.0 will be used Buried polar penalty 0.000 Coulomb vdW cutoff 0.000 H bond cutoff 0.000 Metal-ligand cutoff 10.000 Assigning GlideScore XP5.0 parameters For Glide Extra Precision mode, will use maxref = 800 res reso default 16.0000000000000 16.0000000000000 res reso fin 16.0000000000000 16.0000000000000 Use grow mode-t res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 res reso default 4.00000000000000 4.00000000000000 res reso fin 4.00000000000000 4.00000000000000 REPORT POSE ANCH_2 1 0 43 REPORT POSE ANCH_2 2 0 8 REPORT POSE ANCH_2 3 0 46 REPORT POSE ANCH_2 4 0 14 REPORT POSE ANCH_2 5 0 41 REPORT POSE ANCH_2 6 0 29 REPORT POSE ANCH_2 7 0 10 REPORT POSE ANCH_2 8 0 3 REPORT POSE ANCH_2 9 0 4 REPORT POSE ANCH_2 10 0 5 Full force-field refinement in receptor field for up to 10 poses 10 poses will be postminimized for this ligand iancorig for REPORT pose 1 0 iancorig for REPORT pose 2 0 iancorig for REPORT pose 3 0 iancorig for REPORT pose 4 0 iancorig for REPORT pose 5 0 iancorig for REPORT pose 6 0 iancorig for REPORT pose 7 0 iancorig for REPORT pose 8 0 iancorig for REPORT pose 9 0 iancorig for REPORT pose 10 0 Reporting postminimized pose 2 GlideScore = -8.471 GlideScore( -8.47)+Epik State Penalty( 0.00) = -8.47 kcal/mol DOCKING RESULTS FOR LIGAND 3 (tetramer-1) Best XP pose: 8; GlideScore = -8.47 Emodel = -89.26 E = -53.96 Eint = 0.00 REPORT OF DOCKED POSES The ligand structures were written to the file dock-1lzs-A-nowater-XP-0002_raw.maegz Exiting Glide Date: Friday, August 21 2020, at 10:45:42 PDT CPU time (s): 877.3 user, 13.8 system, 891.9 real Total elapsed time = 892 seconds (14 minutes, 52 seconds) [running at reduced cpu priority] ######## end of dock-1lzs-A-nowater-XP-0002.log #########