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 0m34.445s user 0m0.563s sys 0m0.331s 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 0:1700 spheres. 373. 373. 373. 373. 373. 375. 375. 376. 377. 377. 377. 377. 378. 378. 378. 378. 380. 380. 380. 380. 382. 382. 382. 383. 383. 383. 383. 383. 383. 383. 383. 383. 383. 383. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 384. 385. 385. 385. 385. 385. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 386. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 400. 400. 400. 402. 402. 405. 405. 405. 405. 405. 405. 407. 407. 407. 407. 407. 407. 408. 408. 408. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 409. 410. 410. 410. 410. 410. 410. 410. 410. 412. 412. 412. 412. 412. 412. 415. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 417. 419. 419. 419. 419. 419. 419. 419. 419. 419. 422. 422. 437. 437. 437. 437. 437. 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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: 26 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. 26.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:128) and residue(A:5); changed residue names to "CYX " Created a bond between residue(A:544) and residue(A:538); changed residue names to "CYX " Created a bond between residue(B:589) and residue(B:579); 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 1105 (HEM ), chain 'A'. WARNING mmpdb_write: more than 4 bonds for atom (FE ) in residue 1105 (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 1m7.992s user 0m27.304s sys 0m0.705s Adding spheres to tarted electrostatic grid we had to cook * NE2* we had to cook *HNE2* we had to cook *HNE1* Creating DelPhi electrostatic grid real 0m55.784s user 0m28.095s sys 0m0.737s Creating box around spheres Creating chemgrid maps real 0m44.694s user 0m16.569s sys 0m0.260s Atomic solvent excluded volume calculations underway FORTRAN STOP real 40m28.602s user 16m46.725s sys 0m0.051s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 !!! WARNING: HIZ 357 has a net charge of 0.2000 !!! WARNING: HEM 1105 has a net charge of -4.0000 End of MakeDOCK sphere and grid generation.