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 Post subject: error in docking
PostPosted: Sun Mar 20, 2016 4:36 pm 

Joined: Mon Nov 02, 2015 10:18 am
Posts: 3
I have a problem with docking process

http://www.dockingserver.com/web/docking/319775/


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 Post subject: Re: error in docking
PostPosted: Thu Mar 24, 2016 3:38 pm 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
I have restarted the table generation process, it should fix this error.


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 Post subject: Re: error in docking
PostPosted: Wed Sep 27, 2017 1:43 pm 

Joined: Mon Feb 06, 2017 1:39 pm
Posts: 3
Dear Admin,

I am facing problem in the docking process,
I found the error message.

Prepare docking parameter file – error The error message:
Traceback (most recent call last):
File "tools/prepare_dpf4.py", line 197, in ?
dm.set_ligand(ligand_filename)
File "tools/prepare_dpf4.py", line 55, in set_ligand
self.ligand = Read(ligand_filename)[0]
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/__init__.py", line 51, in Read
molecules = parser.parse()
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/pdbParser.py", line 681, in parse
self.pdbRecordParser[record](records)
File "/usr/lib/python2.4/site-packages/MGLToolsPckgs/MolKit/pdbParser.py", line 1496, in parse_PDB_ROOT
self.mol.ROOT = self.mol.chains.residues.atoms.get(lambda x: x._uniqIndex==0)[0]
File "/usr/lib/python2.4/UserList.py", line 28, in __getitem__
def __getitem__(self, i): return self.data[i]
IndexError: list index out of range.

Kindly inform me, what I have to do for removing the error.
My mail ID- rajesh@bdu.ac.in

Thanks for informing,

regards,
Rajesh


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 Post subject: Re: error in docking
PostPosted: Wed Sep 27, 2017 1:51 pm 

Joined: Mon Feb 06, 2017 1:39 pm
Posts: 3
Dear Admin,

I would like to purchase the 1 month subscription in Docking server. before, I would like to check the docking program in 3 days pack.

I have recently found another error in retrieving ligand from RCSB given below.

Kindly check and inform me. How to fix the error. I would like to buy the 3 days package and use the server.

Mail: rajesh@bdu.ac.in

Download error

Unknown problem while trying to retrieve data from RCSB data.

Thanking you,

Rajesh


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 Post subject: Re: error in docking
PostPosted: Fri Sep 29, 2017 11:25 am 

Joined: Wed Oct 29, 2008 2:24 pm
Posts: 204
Hello, please provide more information to be able to check this issue.


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 Post subject: Re: error in docking
PostPosted: Fri Mar 30, 2018 9:28 am 

Joined: Mon Mar 19, 2018 10:19 am
Posts: 1
Dear sir,

After the ligand and protein were submitted for docking. when I press to start, I receive warning message. What should I do?
but the docking is computing status.
Is it the procedure correct?
Kindly inform me.
Username:rajeshirsea

Thanking you,


Warning: mkdir() [function.mkdir]: Too many links in /sites/virtua/docking/_base/lib/db_file.php on line 101
hiba: /sites/virtua/docking/dockingserver/cache/protein_mozyme.pdbqt/a3 , /sites/virtua/docking/dockingserver/cache/protein_mozyme.pdbqt/
Warning: mkdir() [function.mkdir]: No such file or directory in /sites/virtua/docking/_base/lib/db_file.php on line 101
hiba: /sites/virtua/docking/dockingserver/cache/protein_mozyme.pdbqt/a3 , /sites/virtua/docking/dockingserver/cache/protein_mozyme.pdbqt/a3/
Warning: fopen(/sites/virtua/docking/dockingserver/cache/protein_mozyme.pdbqt/a3/a37c8c93cca3d8b4c8373561d98563a9498baed27185cf987fa4684c9aee5c52.dat) [function.fopen]: failed to open stream: No such file or directory in /sites/virtua/docking/_base/lib/db_file.php on line 127

Warning: fwrite(): supplied argument is not a valid stream resource in /sites/virtua/docking/_base/lib/db_file.php on line 128

Warning: fclose(): supplied argument is not a valid stream resource in /sites/virtua/docking/_base/lib/db_file.php on line 129

Warning: Cannot modify header information - headers already sent by (output started at /sites/virtua/docking/_base/lib/db_file.php:101) in /sites/virtua/docking/_projects/dockingserver/bin/web/docking/index.php on line 1408


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