MakeDOCK 2.0, modified by J.Irwin and M.Mysinger. Previous versions by D.M.Lorber, B.Q.Wei, A.N.Kirschner, and N.Huang Using scripts in /raid5/people/mysinger/xyz/dockenv. Creating binding-site residue list Creating molecular surface real 0m37.198s user 0m0.519s sys 0m0.403s Creating sphgen spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 0:1610 spheres. 404. 404. 404. 405. 405. 405. 405. 405. 427. 427. 427. 427. 427. 427. 427. 427. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 429. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 431. 435. 435. 435. 435. 435. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 438. 439. 442. 442. 442. 442. 445. 445. 445. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 448. 450. 450. 456. 456. 456. 456. 456. 457. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 459. 465. 465. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 466. 469. 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044.4044.4044.4044.4044.4046.4046.4046.4046.4046.4046.4046.4047.4047.4047.4047.4047.5577.5577.5577.5577.5577.5577.5578.5578.5578.5578.5578.5578.5578.5578.5578.5578.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5579.5587.5587.5587.5587.5587.5587.5587.5587.5587.5604.5604.5605.5605.5605.5605.5605.5605.5605.5605.5605.5605.FORTRAN STOP Converting ligand atoms to spheres Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 25 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23. 24. 25.FORTRAN STOP Adding essential hydrogens to receptor Adding all-atom hydrogens... Working on structure 1 Pre-treating metals... Done treating metals Adding hydrogens... Treating metals... Creating di-sulfur bonds... Created a bond between residue(A:15) and residue(A:4); changed residue names to "CYX " Created a bond between residue(A:25) and residue(A:9); changed residue names to "CYX " Created a bond between residue(A:37) and residue(A:27); changed residue names to "CYX " Created a bond between residue(A:127) and residue(A:5); changed residue names to "CYX " Created a bond between residue(A:543) and residue(A:537); changed residue names to "CYX " Created a bond between residue(B:588) and residue(B:578); changed residue names to "CYX " Finding het groups... Coloring atoms by element (green carbons in hets)... Running ProtAssign... using exhaustive mode will sample waters done with preparation Writing to file... DONE. Output file: rec.mae Removing non-polar hydrogens... WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1103 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1103 (HEM ), chain 'B'. Renaming polar hydrogens... Generating matching spheres for delphi Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 120 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.9061.9062.9063.9064.9065.9066.9067.9068.9069.9070.9071.9072.9073.9074.9075.9076.9077.9078.9079.9080.9081.9082.9083.9084.9085.9086.9087.9088.9089.9090.9091.9092.9093.9094.9095.9096.9097.9098.9099.9100.9101.9102.9103.9104.9105.9106.9107.9108.9109.9110.9111.9112.9113.9114.9115.9116.9117.9118.9119.9120.FORTRAN STOP Generating faster matching2 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 45 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.FORTRAN STOP Coloring matching spheres Generating slower matching3 spheres for docking Enter name of sphere cluster file: Enter cluster number to process (<0 = all): Generate surfaces as well as pdb files (/Y)? Enter name for output PDB file name: Cluster 1: 60 spheres. 9001.9002.9003.9004.9005.9006.9007.9008.9009.9010.9011.9012.9013.9014.9015.9016.9017.9018.9019.9020.9021.9022.9023.9024.9025.9026.9027.9028.9029.9030.9031.9032.9033.9034.9035.9036.9037.9038.9039.9040.9041.9042.9043.9044.9045.9046.9047.9048.9049.9050.9051.9052.9053.9054.9055.9056.9057.9058.9059.9060.FORTRAN STOP Coloring matching spheres Adding spheres to electrostatic grid Creating DelPhi electrostatic grid real 1m27.868s user 0m25.526s sys 0m0.714s Adding spheres to tarted electrostatic grid we had to cook * HOG* Creating DelPhi electrostatic grid real 1m37.766s user 0m26.413s sys 0m0.675s Creating box around spheres Creating chemgrid maps real 0m41.055s user 0m15.905s sys 0m0.242s Atomic solvent excluded volume calculations underway FORTRAN STOP real 42m51.055s user 14m10.361s sys 0m0.054s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 !!! WARNING: HIZ 356 has a net charge of 0.2000 !!! WARNING: HEM 1103 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.