######## begin of dock-1d6p-grid-water-r1-0001.log ######### Glide version 87072 (mmshare version 50072) Copyright (c) Schrodinger, LLC. All Rights Reserved. -------------------------------------------------------------------------------- JobId : bambam-0-5f3ff18c Name : dock-1d6p-grid-water-r1-0001 Program : Glide Host : bambam.cchem.berkeley.edu Dir : /scr/kathy/dock-1d6p-grid-water-r1 HostEntry : localhost JobHost : bambam.cchem.berkeley.edu JobDir : /scr/kathy/dock-1d6p-grid-water-r1-0001 JobSchrodinger : /home/mgcf/software-ws/schrodinger2020-2 Commandline : /home/mgcf/software-ws/schrodinger2020-2/glide -RESTART -serial dock-1d6p-grid-water-r1-0001.inp -HOST localhost StartTime : 2020-08-21-09:08:45 -------------------------------------------------------------------------------- [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. GlideScore version SP5.0 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 SP5.0 parameters Postdocking minimization: 5 poses; CvdW cutoffs 100.0 kcal/mol for min, 0.0 kcal/mol for report. GlideScore( -8.37)+Epik State Penalty( 0.00) = -8.37 kcal/mol DOCKING RESULTS FOR LIGAND 1 (chitin) Best Emodel= -99.95 E= -75.33 Eint= 26.49 GlideScore= -8.37 Calling OPLS3e atomtyping ... Finished parameter assignment Number of rotatable bonds 24 Using templates for ring conformations. GlideScore( -6.38)+Epik State Penalty( 0.00) = -6.38 kcal/mol DOCKING RESULTS FOR LIGAND 2 (tetramer-1) Best Emodel= -85.45 E= -64.75 Eint= 17.68 GlideScore= -6.38 REPORT OF DOCKED POSES The ligand structures were written to the file dock-1d6p-grid-water-r1-0001_raw.maegz Exiting Glide Date: Friday, August 21 2020, at 09:14:24 PDT CPU time (s): 317.2 user, 18.7 system, 336.3 real Total elapsed time = 336 seconds (5 minutes, 36 seconds) [running at reduced cpu priority] ######## end of dock-1d6p-grid-water-r1-0001.log ######### ######## begin of dock-1d6p-grid-water-r1-0002.log ######### Glide version 87072 (mmshare version 50072) Copyright (c) Schrodinger, LLC. All Rights Reserved. -------------------------------------------------------------------------------- JobId : bambam-0-5f3ff2e5 Name : dock-1d6p-grid-water-r1-0002 Program : Glide Host : bambam.cchem.berkeley.edu Dir : /scr/kathy/dock-1d6p-grid-water-r1 HostEntry : localhost JobHost : bambam.cchem.berkeley.edu JobDir : /scr/kathy/dock-1d6p-grid-water-r1-0002 JobSchrodinger : /home/mgcf/software-ws/schrodinger2020-2 Commandline : /home/mgcf/software-ws/schrodinger2020-2/glide -RESTART -serial dock-1d6p-grid-water-r1-0002.inp -HOST localhost StartTime : 2020-08-21-09:14:30 -------------------------------------------------------------------------------- [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 28 Using templates for ring conformations. GlideScore version SP5.0 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 SP5.0 parameters Postdocking minimization: 5 poses; CvdW cutoffs 100.0 kcal/mol for min, 0.0 kcal/mol for report. GlideScore( -8.37)+Epik State Penalty( 0.00) = -8.37 kcal/mol DOCKING RESULTS FOR LIGAND 3 (5288898) Best Emodel= -100.32 E= -75.69 Eint= 26.49 GlideScore= -8.37 REPORT OF DOCKED POSES The ligand structures were written to the file dock-1d6p-grid-water-r1-0002_raw.maegz Exiting Glide Date: Friday, August 21 2020, at 09:18:02 PDT CPU time (s): 192.5 user, 16.2 system, 209.2 real Total elapsed time = 209 seconds (3 minutes, 29 seconds) [running at reduced cpu priority] ######## end of dock-1d6p-grid-water-r1-0002.log #########