Cluster Cleaning on DDFE

VDSers,  since some jobs seem to be acting weird and not running fully on the blades – I would suggest doing the Cluster Cleaning protocol that is in the DatabasesVDS folder for EACH blade that you want to run on. You would do this before runnning your job.

Check with a mentor or Dr. B before you do this the first time though.

 

 

How to Clean a Cluster/Rid it of Gold Jobs

By: Adam Nguyen, Clifford Ho, and Kathryn Pendleton

Someone please publish this paper anybody!

This paper is now copyrighted, if you plagiarize from it, we will find you. And kill you.

****************Commands listed to be entered with description of their functions in parentheses********************

1) login to SSH Secure Shell (Host: ddfe.cm.utexas.edu)

2) ganglia cpu_user (should only be running jobs on blades 9-16)

3) ps -u username (ex. ps -u plkrs777)
(This should show you if you have any processes running)

4) ssh compute-0-X (where X=blade number i.e. 9-16, do not input a zero before single digit clusters!!! Enter the       number for computer node that your job is found on, this command will take you to the node )

5) ps -u username (ex. ps -u plkrs777, to see if there are any processes that can be killed from the specific    computer node)

6) kill -9 ######  (To kill a process, use this command, where ###### is the PID number on the left hand side for     the specific process you are trying to get rid of)

7) ps -u username (ex. ps -u plkrs777, this time, to verify that the process is no longer in the list of the       specific computer node)

8) cd /  (This changes your directory to the root directory)

9) cd tmp (This takes you to the temporary directory)

10) ls -l (This displays the long names for each file in the temporary directory, determine which pmvd file is         yours, ie. has your user id)

11) rm pvmd.#### (This command removes the file with the filename specified, ie in this ex it is pmvd.####  WARNING      ONLY DELETE THE pmvd file THAT IS UNDER YOURE USERNAME, DO NOT DELETE SOMEONE ELSES. OR WE WILL FIND YOU AGAIN.      AND KILL YOU AGAIN)

12) rm pvml.#### (This removes the license file)

13) ls -l (To verify the deletion of the file from the temporary directory)

14) exit (to leave the computer node)

15) Repeat steps 1-13 for other nodes requiring cleaning

Suggested order for Virtual Screening Libraries

Here is a list of the libraries we have in the Databases VDS folder as sorted by size.

I would recommend starting with the smaller ones. Only do ones that are in 3d format.

Don’t do the .inx ones. Those are for ICM not GOLD.

This is the size in disk space – not in ligands. So, you will still need to do the LigandCountingInstructions.txt to figure out how many are in there so that you can save 10%.

SIZE                 Name

79091              ION_Channel.inx

937397            cb_306_3d.sdf

1861731          HF9PlatesPlates5_9.sdf

1918122          NIH_ClinCol3Ded.sdf

2197560          MicroFormats.inx

2566387          zincSigmaLibrary3D.sdf

3417571          LOPAC_2d.sdf

3615248          conformersLOPAC_3d.sdf

6314046          LOPAC_3d.sdf

7368555          Fragment-set_3D.sdf

8720108          FragmentLibrary.sdf

17157134        ION_Channel.sdf

18465062        CB-kin_UT.sdf  (this is already 3D)

29809172        ION_Channel3D.sdf

36068862        KINASet.sdf

61269537        KINASet3d.sdf

64466934        HF9_180_Plates_1um3D_catnum.sdf

71529407        MW-set_3D.sdf

76018176        MolecularWeightSet.sdf

123092278      NovaCorePharmaCophore_2.sdf

123632902      NovaCorePharmaCophore_1.sdf

123989001      DIVERSet.sdf

127822631      NovaCorePharmaCophore_4.sdf

134109995      NovaCorePharmaCophore_3.sdf

139679653      ChemBridge-diversity3D.sdf

139679653      ChemBridge-diversity.sdf

153754871      CNS-Set.sdf

181460186      MayBridge50k_3D.sdf

271201171      CNS-Set3d.sdf

499025027      MicroFormats.sdf

508657806      NOVACore-PHARMACophore_Combined.sdf

900813568      MicroFormats3D.sdf

SIZE	Name
79091	ION_Channel.inx
937397	cb_306_3d.sdf
1861731	HF9PlatesPlates5_9.sdf
1918122	NIH_ClinCol3Ded.sdf
2197560	MicroFormats.inx
2566387	zincSigmaLibrary.sdf
3417571	LOPAC_2d.sdf
3615248	conformersLOPAC_3d.sdf
6314046	LOPAC_3d.sdf
7368555	Fragment-set_3D.sdf
8720108	FragmentLibrary.sdf
17157134	ION_Channel.sdf
18465062	CB-kin_UT.sdf
29809172	ION_Channel3D.sdf
36068862	KINASet.sdf
61269537	KINASet3d.sdf
64466934	HF9_180_Plates_1um3D_catnum.sdf
71529407	MW-set_3D.sdf
76018176	MolecularWeightSet.sdf
123092278	NovaCorePharmaCophore_2.sdf
123632902	NovaCorePharmaCophore_1.sdf
123989001	DIVERSet.sdf
127822631	NovaCorePharmaCophore_4.sdf
134109995	NovaCorePharmaCophore_3.sdf
139679653	ChemBridge-diversity3D.sdf
139679653	ChemBridge-diversity.sdf
153754871	CNS-Set.sdf
181460186	MayBridge50k.sdf
271201171	CNS-Set3d.sdf
499025027	MicroFormats.sdf
508657806	NOVACore-PHARMACophore_Combined.sdf
900813568	MicroFormats3D.sdf

Journal Club 4

The new journal article has been uploaded to GDocs. Print it, read it 2x, and bring it to class.

https://docs.google.com/fileview?id=0B_Gl3lMyhDsoYTU1Nzc3ZGUtZGQwYS00Njg5LTg2ZjYtMjAxNjRjZTBjMzVm&hl=en&authkey=CI-5gNEB

PS: if you want to ask others in the group about the paper before class – this is a good place to post questions and answers in the comments after these posts.

That may better prepare you for the quiz questions.

Study Questions:

1. What EC number for this enzyme?
2. What is peptidoglycan and why is it important to bacteria? Do you have it in your body?
3. What is special about the ‘D’ in D-Ala-D-Ala ?
4. What two methods were used to assay efficacy of these inhibitors? What are the advantages of each over the other?
5. What is missing in Figures 3b,c, and d ?
6. Why do they test both E. coli and S. aureus?
7. What would be a next step after this research?

ACA 1.126 schedule computer lab

http://www.biosci.utexas.edu/reservations/default.aspx

Times when ACA 1.126 computer lab is occupied

Should have SSH, Putty, Xming, PyMol  – yeah!

Posts and Virtual Setup

Text only posts are boring!  – each VDSers should shoot for including at least 1 image per week in their posts.

Also, Tuesday after class – there will be a computer lab session to set up your Targets for Virtual Screening (should take 30 min- 1.5 hrs). You can’t start this until you have finished your Virtual Screen Refresher – so this would also be a good time to get help on that. We’ll have another session for this later – so don’t worry if you can’t make this one.

You can also use this time to ask questions about your Research Report on Target. -e.g. finding info about your enzyme or how to propose doing work on your target.

Virtual Screen Refresher

Please post a table of the top 10 compounds from your Virtual Screen refresher once you have finished it. Say briefly what you did (we all did the same thing) but also say which library you used. Some poeple used a different one I think.