%IMPACT-I (openwt): Request to open FORMATTED file dock_scalingon_amideon.out on unit 2 Glide version 40108 mmshare version 15106 Copyright (c) 2005 Schrodinger, LLC. All Rights Reserved. Host: IRIX64 hyperion 6.5 10100655 IP35 JobId: hyperion-0-438e5d69 SCHRODINGER directory: /schrodinger IMPACT_EXEC directory: /schrodinger/impact-v40108/bin/IRIX-mips4 MMSHARE_EXEC directory: /schrodinger/mmshare-v15107/bin/IRIX-mips4 VdW radii of ligand atoms scaled by 0.8000000000000000 Charge cutoff for polarity 0.1500000000000000 GLIDE CONSTRAINTS APPLIED ------------------------- 1 out of 1 constraints used from file /glide/cdk2/grids_cdk2.cons Labels and receptor types of constraints used are: (Constraint1) (H-bond Donor) All docked poses must satisfy all of the above constraints After readscreen, (nx, ny, nz) = ( 26, 26, 26). Receptor setup: (nsites, nx, ny, nz, bsize) = ( 216, 26, 26, 26, 1.000000000000000 ). Screening setup finished. DOCKMAIN: getting receptor. %IMPACT-I (xdrrd): File /glide/cdk2/grids_cdk2.grd opened for reading DOCKMAIN after grid: (nx, ny, nz) = ( 64, 64, 64 ). %IMPACT-I (xdrrd): File /glide/cdk2/grids_cdk2_coul2.fld opened for reading %IMPACT-I (xdrrd): File /glide/cdk2/grids_cdk2_vdw.fld opened for reading %IMPACT-I (xdrrd): File /glide/cdk2/grids_cdk2.gsc opened for reading DOCKMAIN: Grid setup finished %IMPACT-I(foldmain): calling opls2001 atomtyping ... %IMPACT-I(foldmain): finished parameter assignment ** Entering Conformation Generator ** Amide bond rotations turned off Number of rotatable bonds 7 Core rotatable bonds, max cores 7 214 Buried polar penalty 0.000 Coulomb vdW cutoff 0.000 H bond cutoff 0.000 Metal-ligand cutoff 0.000 Assigning OPLS_2001 GlideScore SP4.0 parameters Checked constraints after refinement with max HB dsq = 16.00000000000000 After refinement, constraint filter reduced number of poses from 500 to 311. Total constraint copies over all poses = 344 Constraint(s) matched for ligand 1, pose 14 Score = -7.623 Emodel = -86.910 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 303 Score = -7.855 Emodel = -85.416 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 17 Score = -7.732 Emodel = -82.464 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 53 Score = -7.808 Emodel = -81.496 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 7 Score = -7.414 Emodel = -79.418 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 75 Score = -7.576 Emodel = -77.902 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 192 Score = -7.237 Emodel = -75.878 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 39 Score = -6.869 Emodel = -75.833 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 291 Score = -7.025 Emodel = -75.058 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 24 Score = -6.872 Emodel = -73.704 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 79 Score = -6.365 Emodel = -64.876 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 229 Score = -6.277 Emodel = -64.207 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 15 Score = -6.434 Emodel = -64.109 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 141 Score = -5.527 Emodel = -62.499 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 315 Score = -5.718 Emodel = -58.274 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) Constraint(s) matched for ligand 1, pose 82 Score = -5.110 Emodel = -51.534 This pose satisfies at least the following constraint(s). (Constraint1) (Type = H-bond Donor) DOCKING RESULTS FOR LIGAND 1 (CN5CCN(Cc4ccc(C(=O)Nc3cccc(Nc2nccc(c1cccnc1)n2)c3)cc4)CC5) Except for Best Emodel, the poses reported here may not satisfy the user-specified constraints. Lowest Efinal = -57.74 Eint= 5.13 Glidescore = -9.62, from pose 84, conf 174, lig 1 Best Emodel = -86.91 E = -54.53 Eint = 4.62 Glidescore = -7.62 from pose 14, conf 16, lig 1 Glide is executing the glide_sort command. Command-line equivalent is: /schrodinger/utilities/glide_sort -n 20 -o dock_cdk2_lib.mae -r dock_cdk2.rept -use_gscore -norecep -hbond_cut 0.00 -cvdw_cut 0.00 -metal_cut 0.00 dock_cdk2_raw.mae REPORT OF BEST 20 POSES The sorted ligand structures were written to the file dock_cdk2_lib.mae Final rankings based on GlideScore 4 poses were rejected by the energy filters, Coul+vdw Energy <= 0.0 Hbond Interaction <= 0.0 Metal Interaction <= 0.0 glide_sort command succeeded. Output is in files dock_cdk2_lib.mae and dock_cdk2.rept %IMPACT-I (timit): Total CPU time = 96.48 seconds ( 1.6 minutes)