Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-6-09.c.bkslab.org du2 starts 1 molecule processed, 0 errors first try already in then inzinc count is 0 bzcat: Can't open input file 34: No such file or directory. bzcat: Can't open input file 21: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 bzcat: Can't open input file 45: No such file or directory. bzcat: Can't open input file 82: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. bzcat: Can't open input file 34: No such file or directory. bzcat: Can't open input file 21: No such file or directory. bzcat: Can't open input file 45: No such file or directory. bzcat: Can't open input file 82: No such file or directory. du2.csh script updated ligand processing Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 147, in ? result = server.decoys(data) File "/usr/lib64/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib64/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib64/python2.4/xmlrpclib.py", line 1147, in request return self._parse_response(h.getfile(), sock) File "/usr/lib64/python2.4/xmlrpclib.py", line 1286, in _parse_response return u.close() File "/usr/lib64/python2.4/xmlrpclib.py", line 744, in close raise Fault(**self._stack[0]) xmlrpclib.Fault: 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 0m2.445s user 0m0.336s sys 0m0.162s 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 0:1058 spheres. 109. 110. 110. 110. 111. 111. 111. 111. 111. 111. 111. 111. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 113. 114. 114. 128. 128. 128. 128. 128. 128. 128. 128. 128. 128. 129. 129. 129. 129. 129. 129. 130. 130. 130. 130. 130. 137. 138. 138. 138. 142. 142. 142. 142. 142. 146. 146. 378. 378. 380. 380. 380. 380. 380. 380. 380. 380. 380. 380. 384. 384. 384. 384. 384. 384. 384. 418. 418. 418. 418. 418. 418. 418. 419. 422. 422. 424. 424. 424. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 428. 429. 429. 429. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 431. 433. 436. 436. 436. 436. 436. 436. 436. 436. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 437. 438. 451. 451. 451. 451. 452. 452. 452. 452. 453. 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778. 778. 778. 778. 778. 778. 778. 778. 783. 783. 786. 794. 794. 797. 797. 798. 813. 813. 814. 823. 823. 823. 823. 823. 823. 823. 824. 824. 824. 824. 824. 824. 831. 831. 881. 881. 881. 881. 881. 881. 881. 881. 881. 881. 881. 881. 881. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 882. 883. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 893. 896. 899. 899. 899. 901. 902. 902. 902. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 911. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912. 912.1171.1171.1171.1171.1171.1171.1183.1183.1183.1183.1187.1198.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1199.1209.1209.1209.1209.1209.1209.1209.1209.1209.1212.1212.1212.1214.1215.1215.1215.1215.1216.1216.1216.1216.1217.1217.1217.1217.1217.1217.1217.1217.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1218.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1219.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1220.1222.1223.1223.1228.1253.1256.1256.1256.1256.1256.1256.1256.1429.1429.1429.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1430.1431.1431.1431.1431.1431.1431.1431.1431.1431.1431.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1432.1433.1433.1433.1434.1434.1434.1434.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1437.1440.1440.1440.1440.1440.1440.1444.1444.1444.1444.1444.1444.1444.1444.1444.1444.1444.1444.1444.1445.1445.1445.1445.1445.1445.1446.1446.1446.1446.1447.1449.1449.1449.1449.1454.1455.1455.1455.1455.1456.1456.1456.1456.1456.1456.1456.1456.1456.1456.1456.1456.1456.1458.1460.1460.1460.1460.1460.1460.1460.1460.1460.1460.1462.1463.1463.1463.1463.1463.1463.1464.1464.1464.1654.1654.1654.1654.1654.1654.1654.1654.1657.1657.1657.1657.1657.1657.1657.1657.1657.1657.1672.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1675.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1676.1677.1677.1677.1677.1681.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1683.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.1684.2071.2071.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2073.2074.2074.2074.2074.2074.2074.2074.2074.2074.2074.2074.2074.2074.2074.2074.2076.2076.2076.2076.2076.2076.2076.2076.2076.2076.2076.2076.2076.2076.2278.2278.2278.2278.2278.2278.2278.2278.2278.2278.2278.2278.2278.2281.2281.2281.2281.2281.2281.2281.2281.2287.2287.2288.2288.2288.2288.2288.2288.2288.2288.2295.2295.2295.2296.2297.2297.2297.2297.2297.2297.2297.2297.2300.2301.2302.2302.2302.2302.2302.2302.2302.2302.2302.2302.2306.2306.2324.2324.2324.2324.2324.2324.2324.2324.2324.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: 23 spheres. 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22. 23.FORTRAN STOP Adding essential hydrogens to receptor 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 0m27.819s user 0m26.063s sys 0m0.699s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m27.726s user 0m25.831s sys 0m0.722s Creating box around spheres Creating chemgrid maps real 0m24.030s user 0m23.069s sys 0m0.255s Atomic solvent excluded volume calculations underway FORTRAN STOP real 22m43.546s user 22m38.745s sys 0m0.269s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. File name = ../grids/distmap In source file scoreopt_so.f, at line number 625 PGFIO-F-209/OPEN/unit=2/'OLD' specified for file which does not exist. 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