Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-1-08.c.bkslab.org du2 starts 1 molecule processed, 0 errors convert.py (MDL SDF -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. mol2nam v1.9 Structure to Name Conversion OpenEye Scientific Software, February 2009 convert.py (Tripos MOL2 -> Isomeric SMILES): mols in: 1 mols out: 1 Total: 1 mols processed. first try already in then inzinc count is 0 bzcat: Can't open input file 63: No such file or directory. bzcat: Can't open input file 25: No such file or directory. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 88: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 2 mols out: 2 Total: 2 mols processed. count is 0 bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 90: No such file or directory. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 92: No such file or directory. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 94: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 3 mols out: 3 Total: 3 mols processed. bzcat: Can't open input file 63: No such file or directory. bzcat: Can't open input file 25: No such file or directory. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 88: No such file or directory. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 90: No such file or directory. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 92: No such file or directory. bzcat: Can't open input file 59: No such file or directory. bzcat: Can't open input file 94: No such file or directory. du2.csh script updated ligand processing 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 0m3.724s user 0m0.593s sys 0m0.547s 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 0:1161 spheres. 166. 166. 166. 170. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 174. 176. 176. 176. 176. 176. 176. 184. 184. 184. 184. 184. 184. 195. 197. 197. 205. 205. 205. 205. 205. 206. 206. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 208. 386. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 387. 388. 388. 388. 388. 388. 388. 388. 388. 388. 388. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 392. 394. 394. 394. 394. 394. 394. 394. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 395. 396. 396. 397. 398. 398. 398. 398. 398. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 399. 401. 401. 401. 401. 403. 403. 403. 403. 406. 406. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 407. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 410. 411. 411. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 412. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 414. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 420. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 422. 425. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 430. 431. 432. 432. 433. 433. 433. 433. 433. 433. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 434. 440. 440. 440. 440. 493. 493. 498. 498. 505. 512. 512. 512. 512. 512. 512. 512. 568. 568. 568. 592. 592. 622. 622. 622. 622. 622. 622. 622. 622. 622. 622. 624. 624. 624. 624. 624. 624. 624. 624. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 625. 626. 626. 627. 627. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 628. 632. 636. 639. 639. 639. 640. 640. 640. 640. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 642. 644. 644. 644. 644. 644. 644. 645. 646. 646. 646. 646. 646. 646. 647. 647. 647. 647. 647. 647. 648. 648. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 649. 650. 660. 660. 660. 660. 660. 660. 660. 660. 662. 662. 662. 662. 662. 662. 662. 663. 664. 664. 664. 664. 668. 668. 669. 671. 674. 675. 675. 675. 676. 676. 676. 678. 679. 679. 679. 679. 679. 680. 680. 680. 680. 680. 680. 680. 680. 680. 680. 680. 680. 680. 680. 680. 680. 680. 681. 681. 686. 688. 688. 688. 688. 694. 694. 694. 694. 694. 694. 694. 694. 695. 695. 695. 695. 695. 695. 695. 695. 695. 695. 699. 699. 740. 740. 762. 762. 763. 763. 763. 763. 763. 763. 763. 763. 763. 773. 773. 773. 773. 773. 773. 773. 775. 775.1078.1078.1078.1079.1079.1079.1079.1079.1079.1079.1079.1079.1079.1079.1082.1082.1082.1082.1083.1083.1083.1083.1084.1085.1085.1085.1085.1085.1085.1085.1087.1088.1092.1093.1093.1093.1093.1093.1106.1110.1110.1110.1110.1110.1110.1263.1263.1264.1264.1264.1264.1264.1264.1264.1264.1276.1285.1286.1287.1287.1287.1287.1287.1287.1287.1289.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1290.1292.1292.1292.1292.1292.1292.1292.1292.1292.1292.1292.1292.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1306.1314.1314.1316.1316.1316.1316.1316.1316.1316.1316.1317.1317.1317.1318.1318.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1319.1320.1320.1320.1320.1320.1320.1320.1320.1320.1344.1344.1347.1347.1545.1545.1558.1568.1571.1934.1934.1934.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1935.1936.1936.1936.1936.1936.1936.1937.1937.1937.1937.1937.1937.1937.1941.1941.1941.1941.1941.1941.1941.1941.1941.1941.1941.1943.1947.1947.1947.1949.1950.1950.1950.1950.1950.1950.1951.1951.1951.1951.1951.1951.1951.1951.1951.1951.1951.1951.1951.1951.1951.1951.1952.1952.1952.1952.1952.1952.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1953.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1954.1955.1955.1955.1957.1957.1957.1957.1958.1958.1958.1958.1958.1958.1958.1958.1958.1958.1961.1961.1961.1961.1964.1964.1964.1964.1964.1964.1964.1964.1964.1964.1966.1970.1970.1970.1971.1971.1971.1971.1971.1971.1972.1972.1972.1972.1972.1972.1972.1972.1972.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1973.1978.1979.1979.1982.1982.1982.1983.1983.1983.1983.1986.1986.1986.1986.1986.1986.1986.1986.1986.1986.1986.1986.1986.1986.2240.2240.2240.2240.2240.2240.2240.2240.2245.2245.2245.2246.2246.2246.2246.2246.2246.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2257.2260.2260.2260.2260.2260.2260.2260.2260.2260.2260.2260.2260.2261.2574.2574.2574.2574.2574.2574.2574.2574.2574.2574.2575.2575.2575.2575.2575.2575.2575.2575.2575.2575.2575.2575.2575.2575.2576.2576.2576.2578.2578.2578.2578.2578.2579.2579.2579.2579.2579.2579.2582.2582.2582.2582.2582.2584.2584.2588.2588.2588.2588.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: 32 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. 27. 28. 29. 30. 31. 32.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 we had to cook * OP2* we had to cook * OP1* we were asked to cook * CB * *CXM* 22 we had to cook * CG * we had to cook * CN * we had to cook * ON2* we had to cook * ON1* we were asked to cook * SD * * SD* 22 we were asked to cook * CE * * CE* 22 Creating DelPhi electrostatic grid real 0m32.948s user 0m30.419s sys 0m0.963s Adding spheres to tarted electrostatic grid we had to cook * OP2* we had to cook * OP1* we were asked to cook * CB * *CXM* 22 we had to cook * CG * we had to cook * CN * we had to cook * ON2* we had to cook * ON1* we were asked to cook * SD * * SD* 22 we were asked to cook * CE * * CE* 22 Creating DelPhi electrostatic grid real 0m33.555s user 0m30.479s sys 0m0.942s Creating box around spheres we had to cook * OP2* we had to cook * OP1* we were asked to cook * CB * *CXM* 22 we had to cook * CG * we had to cook * CN * we had to cook * ON2* we had to cook * ON1* we were asked to cook * SD * * SD* 22 we were asked to cook * CE * * CE* 22 Creating chemgrid maps real 0m55.255s user 0m54.360s sys 0m0.358s Atomic solvent excluded volume calculations underway FORTRAN STOP real 28m57.332s user 28m54.938s sys 0m0.213s Checking for WARNINGS in OUTPARM. WARNING--parameters not found for ATOM 3154 OP3 UMP 529 sqrt(A), sqrt(B), and charge set to 0.0 Checking for WARNINGS in delphi.log. !!! WARNING: UMP 529 has a net charge of -0.1000 !!! WARNING: UMP 529 has a net charge of -0.1000 !!! WARNING: UMP 529 has a net charge of -0.1000 End of MakeDOCK sphere and grid generation. Grid preparation completed normally. Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar Traceback (most recent call last): File "/raid5/people/mysinger/xyz/dockenv/etc/xmlclient.py", line 65, in ? result = server.qsubset(data, 'db') 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 1129, in request self.send_content(h, request_body) File "/usr/lib64/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib64/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib64/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib64/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib64/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar going into second inactives test after second inactives finished ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied, please try again. ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied, please try again. ssh_askpass: exec(/usr/libexec/openssh/ssh-askpass): No such file or directory Permission denied (publickey,gssapi-with-mic,password). FILTER PROGRAM THIS PROGRAM FILTERS ATOMIC COORDINATE FILES BASED ON DISTANCE AND SEQUENCE CRITERIA name of file to filter by - xtal-lig.pdb filter by atom names or numbers in receptor(na/nu)? residue/ligand orientation number increment filter? -100000 Filter for MS run?(Y/N) N Either names or numbers of the atoms to filter by, as they appear in the pdb, with boolean and/or operators if such apply between them. Maximum of one boolean per two filter atoms. name of ligand file- rec.pdb names of ligand atoms to match against receptor filters. Include boolean and/ors between EACH atom specified. LIGAND ATOM 1ISALL internal filtering? Y distance cutoffs for each of the receptor atoms specified- 25.00000 output filename- poc.txt number of allowed ligand contacts in an all-filter? LIGBUM IS- 0 IR IS 51 Number of atoms in ligand - 0 IL IS 2590 NR IS- 1 INTERNAL BEGUN INTERNAL COMPLETED 23 NUMLIG IS- 23 TOTAL NUMBER OF ORIENTATIONS WRITEN IS - 1 filtering complete mf7.csh - site preparation complete, preliminary docking queued