How can I solve the problem?

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How can I solve the problem?

Postby ysohn » Thu Feb 14, 2013 5:20 pm

I want to perform molecular docking simulation with manganese ion contained protein

When I tried simulation using PyRx, it cannot define the ion.

How can I solve the problem?

Plz give me an answer.
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Re: How can I solve the problem?

Postby sargis » Fri Feb 15, 2013 4:26 pm

Thanks for the message. What do you mean by it cannot define the ion?
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Re: How can I solve the problem?

Postby ysohn » Sat Feb 16, 2013 3:35 am

I cannot perform molecular docking simulation with manganese ion using PyRx.

Please give me the answer.
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Re: How can I solve the problem?

Postby sargis » Sat Feb 16, 2013 5:19 am

ysohn wrote:I cannot perform molecular docking simulation with manganese ion using PyRx.

Please give me the answer.

If you are loosing manganese ion when creating pdbqt from manganese ion contained protein, please see Losing Zinc metal in Macromolecule when converting to PDBQT for a possible solution for this problem.

Hope this helps.
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Re: How can I solve the problem?

Postby ysohn » Sat Feb 16, 2013 8:38 am

Thank you for your kind explanation. But it's not work.

Maybe another problem exists to simulate with metal ion.

The error message is like this.

Error in : <bound method RunAutoGrid.TryRun of <PyRx.autogridPage.RunAutoGrid; proxy of <Swig Object of type 'wxPanel *' at 0xb5d93c0> >>
Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> Sorry, there are no Gasteiger parameters available for atom Final_MN_1:A: MN270:MN
Sorry, there are no Gasteiger parameters available for atom Final_MN_1:A: MN271:MN
>>> Traceback (most recent call last):
File "C:\Program Files\lib\site-packages\PyRx\wxMainFrame.py", line 304, in TryCommand
retObject = command(*args, **kw)
File "C:\Program Files\lib\site-packages\PyRx\autogridPage.py", line 229, in TryRun
self.processPanel.Start()
File "C:\Program Files\lib\site-packages\PyRx\webServices.py", line 657, in Start
resp = self.appServicePort.launchJob(self.req)
File "C:\Program Files\lib\site-packages\PyRx\AppService\AppService_client.py", line 60, in launchJob
response = self.binding.Receive(launchJobResponse.typecode)
File "C:\Program Files\lib\site-packages\ZSI\client.py", line 536, in Receive
return _Binding.Receive(self, replytype, **kw)
File "C:\Program Files\lib\site-packages\ZSI\client.py", line 455, in Receive
raise FaultException(msg)
FaultException: The AXIS engine could not find a target service to invoke! targetService is autogrid
opal-server-0-0-0.local
>>>

And the part of manganese in my pdf file is like this.

ATOM 2037 N LEU A 269 50.605 -27.549 52.654 1.00 61.92 A N
ATOM 2038 CA LEU A 269 51.593 -26.488 52.463 1.00 63.76 A C
ATOM 2039 CB LEU A 269 51.024 -25.148 52.951 1.00 64.47 A C
ATOM 2040 CG LEU A 269 49.550 -24.822 52.663 1.00 66.20 A C
ATOM 2041 CD1 LEU A 269 49.216 -23.461 53.264 1.00 64.95 A C
ATOM 2042 CD2 LEU A 269 49.264 -24.844 51.164 1.00 65.49 A C
ATOM 2043 C LEU A 269 52.907 -26.781 53.195 1.00 64.61 A C
ATOM 2044 O LEU A 269 53.420 -25.861 53.871 1.00 65.24 A O
ATOM 2045 OXT LEU A 269 53.419 -27.917 53.074 1.00 64.38 A O
ATOM 2046 MN MN A 270 23.722 -39.484 62.251 1.00 36.06 A MN
ATOM 2047 MN MN A 271 23.783 -43.760 62.323 1.00 38.08 A MN
TER 2048 MN A 271
END

How can I perform molecular docking simulation with this protein? Please, help me.
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Re: How can I solve the problem?

Postby sargis » Sat Feb 16, 2013 4:24 pm

You are welcome. The error message when using remote execution mode is a know issue - http://pyrx.sourceforge.net/downloads/71-known-issues

I'm planning to include AutoDock binaries with PyRx and remove the Remote execution mode in the next release. Unfortunately, I won't have time to make the next release anytime soon. See also: http://sourceforge.net/apps/trac/pyrx/roadmap
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