Enabling DOCK Developer Scripts incl Database Preparation Intel/Linux inactives we got past inactivesDB.ism actives we got past actives.ism node-3-28.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. mid: No such file or directory. hi: No such file or directory. lo: No such file or directory. mid: No such file or directory. first try already in then inzinc count is 0 bzcat: Can't open input file 53: No such file or directory. bzcat: Can't open input file 33: No such file or directory. convert.py (Tripos MOL2 -> MDL SDF): mols in: 1 mols out: 1 Total: 1 mols processed. count is 0 nothing to compress bzcat: Can't open input file 53: No such file or directory. bzcat: Can't open input file 33: No such file or directory. nothing to compress 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 0m2.249s user 0m0.411s sys 0m0.282s 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 0:1956 spheres. 112. 112. 112. 112. 112. 112. 113. 113. 113. 113. 113. 114. 114. 114. 114. 114. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 115. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 116. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 117. 118. 118. 118. 118. 118. 118. 119. 119. 119. 119. 122. 122. 122. 122. 122. 122. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 123. 124. 124. 124. 124. 124. 124. 125. 125. 125. 125. 125. 125. 125. 127. 127. 127. 127. 127. 127. 127. 130. 130. 130. 130. 131. 131. 131. 131. 131. 132. 132. 132. 132. 132. 137. 137. 137. 138. 138. 139. 139. 139. 139. 139. 139. 139. 146. 146. 146. 146. 146. 151. 151. 152. 152. 152. 152. 152. 153. 153. 153. 153. 153. 153. 153. 154. 154. 154. 154. 154. 154. 154. 159. 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611. 617. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 619. 621. 621. 623. 627. 627. 627. 627. 627. 629. 630. 630. 630. 631. 631. 631. 631. 631. 631. 631. 631. 634. 634. 635. 637. 637. 637. 637. 637. 637. 637. 637. 637. 637. 637. 638. 638. 638. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 639. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 641. 648. 648. 650. 650. 650. 650. 651. 651. 651. 651. 651. 651. 654. 654. 654. 655. 655. 655. 655. 655. 655. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 656. 658. 659. 659. 659. 659. 659. 659. 661. 661. 661. 663. 663. 663. 663. 663. 664. 664. 668. 668. 668. 668. 669. 670. 670. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 673. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 676. 677. 677. 677. 677. 677. 677. 677. 677. 677. 677. 677. 677. 684. 685. 685. 685. 685. 686. 687. 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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: 28 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.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: 108 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.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 0m41.285s user 0m38.466s sys 0m1.522s Adding spheres to tarted electrostatic grid Creating DelPhi electrostatic grid real 0m41.198s user 0m38.408s sys 0m1.508s Creating box around spheres Creating chemgrid maps real 1m53.785s user 1m9.069s sys 0m0.609s Atomic solvent excluded volume calculations underway FORTRAN STOP real 29m29.458s user 29m28.974s sys 0m0.273s Checking for WARNINGS in OUTPARM. Checking for WARNINGS in delphi.log. End of MakeDOCK sphere and grid generation. Grid preparation completed normally. not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready 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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/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/lib/python2.4/xmlrpclib.py", line 1096, in __call__ return self.__send(self.__name, args) File "/usr/lib/python2.4/xmlrpclib.py", line 1383, in __request verbose=self.__verbose File "/usr/lib/python2.4/xmlrpclib.py", line 1129, in request self.send_content(h, request_body) File "/usr/lib/python2.4/xmlrpclib.py", line 1243, in send_content connection.endheaders() File "/usr/lib/python2.4/httplib.py", line 804, in endheaders self._send_output() File "/usr/lib/python2.4/httplib.py", line 685, in _send_output self.send(msg) File "/usr/lib/python2.4/httplib.py", line 652, in send self.connect() File "/usr/lib/python2.4/httplib.py", line 636, in connect raise socket.error, msg socket.error: (111, 'Connection refused') slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar not ready slept 360 waiting for similar failed to get similars