[Dock-fans] Fwd: Sphere Selector Error

Trent E. Balius tbalius at aol.com
Fri Jun 24 15:51:57 PDT 2011



Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Benny Lo <benny_yc_lo at yahoo.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Fri, Jun 24, 2011 3:00 pm
Subject: Re: Sphere Selector Error




Hi, Trent:
Thanks, moving model with Chimera works.
-Ben

--- On Fri, 6/24/11, Trent E. Balius <tbalius at aol.com> wrote:


From: Trent E. Balius <tbalius at aol.com>
Subject: Re: Sphere Selector Error
To: benny_yc_lo at yahoo.com, dock-fans at mailman.docking.org
Date: Friday, June 24, 2011, 7:25 AM


 Hi Ben,

Try and take the original PDB complex translate the center of mass of the protein to the origin (0,0,0) and rerun everything. Use a program (like chimera) to translate (use the move command).  This should solve the problem.

other things to try:
I would suggest copying all files you need into your current directory including the executables.
You could also try running dock on a different machine perhaps there is an issue with the compilation?


Please try all of the suggestions.

I am at a bit of a loss for other suggestions. 

I am sending the message to the dock-fans at mailman.docking.org. Perhaps someone else on  the dock-fans mailing list will have some other suggestions?

Good luck,

 

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Benny Lo <benny_yc_lo at yahoo.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Thu, Jun 23, 2011 7:38 pm
Subject: Re: Sphere Selector Error




Hi, Trent:

I have recompiled the executable and ran the same script_demo I sent you in 2_site folder and received the following message:

/Desktop/dock6/tutorials/STARD9/2_site$ ./script_demo
 Enter name of sphere cluster file:
 Enter cluster number to process (<0 = all):  Generate surfaces as well as pdb files (<N>/Y)?  Enter name for output PDB file name:

Cluster  1:   0 spheres.

 Enter name of sphere cluster file:
 Enter cluster number to process (<0 = all):  Generate surfaces as well as pdb files (<N>/Y)?  Enter name for output PDB file name:

Cluster  1:  82 spheres
  60.  63.  78.  79.  82.  87.  88.  89.  90.  92.  97.  98. 109. 112. 115. 117. 119. 121. 123. 124. 145. 147. 156. 157. 336. 517. 521. 537. 538. 539. 584. 594. 598. 600. 609. 812. 816. 821. 823. 825. 827. 829. 831. 837. 845. 846. 849. 852. 853. 860. 861. 862. 863. 865. 917. 961.1648.1679.1680.1681.1685.1690.1714.1730.1732.1740.1980.1997.1998.2020.2023.2024.2031.2042.2046.2051.2065.2067.2082.2083.2085.2141.

what is your output like ? I am running the original sphgen.  Maybe there is something wrong with my sphere_selector?  

-Ben

--- On Thu, 6/23/11, Trent E. Balius <tbalius at aol.com> wrote:


From: Trent E. Balius <tbalius at aol.com>
Subject: Re: Sphere Selector Error
To: benny_yc_lo at yahoo.com
Date: Thursday, June 23, 2011, 3:54 PM


Hi Ben,

I was able to run the new files fine.

If all else fail, Try and take the original PDB complex translate the center of mass of the protein to the origin (0,0,0) and rerun everything.  This should solve the problem.

First you could try the following:

I would suggest copying all files you need into your current directory including the executables.

Try recompiling dock in a new directory.

 
Questions:
  Is the problem running sphere_selector?
  
What version are you using the original?  Do not use the modified version I sent. 
  
I am at a bit of a loss. 


Trent


 

-----Original Message-----
From: Benny Lo <benny_yc_lo at yahoo.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Thu, Jun 23, 2011 6:08 pm
Subject: Re: Sphere Selector Error




Hi, Trent:

Thank you for your help. I tried to use the sed command you suggested but the program still doesn't pick up any spheres. I have resaved the ligand mol2 file to make sure they are within the generated cluster. Please see the attached file for the updated mol2 and script file. I still don't know what went wrong.

Please  help.

Thank you,
Ben  


--- On Thu, 6/23/11, Trent E. Balius <tbalius at aol.com> wrote:


From: Trent E. Balius <tbalius at aol.com>
Subject: Re: Sphere Selector Error
To: benny_yc_lo at yahoo.com
Date: Thursday, June 23, 2011, 11:44 AM


Doing the following:

sed 's/-/ -/g' rec.1.sph > new.sph
 
./sphere_selector new.sph lig_charged.mol2 10

worked for me:

The selected_spheres produced are as follows:

DOCK spheres within 10 ang of ligands
cluster     1   number of spheres in cluster   109
   79 -43.72933-153.22035  72.21230   1.400  774 0  0
  105 -45.99810-150.65045  72.51203   2.174  121 0  0


 

Trent 

 

 

-----Original Message-----
From: Benny Lo <benny_yc_lo at yahoo.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Thu, Jun 23, 2011 2:25 pm
Subject: Re: Sphere Selector Error




Hi, Trent:

I tried the sphgen_cpp but doesn't working either. I tried sed to add space between x and y coordinate: 

sed 's/[^ ]-/ -/g' rec.sph > new.sph

although it generate selected_sphere.pdb, it doesn't selected any spheres from the cluster:
 
Cluster  1:   0 spheres.

I tried to open both ligand and spheres in chimera and found that the ligand is not in the cluster, it is correct?

Please help,
Thank you. 
 
-Ben


--- On Thu, 6/23/11, Trent E. Balius <tbalius at aol.com> wrote:


From: Trent E. Balius <tbalius at aol.com>
Subject: Re: Sphere Selector Error
To: benny_yc_lo at yahoo.com, dock-fans at mailman.docking.org
Date: Thursday, June 23, 2011, 3:52 AM


 Hi Ben,

Perhaps, sending you a modified  sphere_selector.cpp program was premature.
Use the unmodified version.  Sorry for the confusion. 

Try the following:

(1) download  from the following page and use sphgen.cpp:

http://dock.compbio.ucsf.edu/Contributed_Code/sphgen_cpp.htm

I think using this program will fix your problem.

if (1) does not work try the following:

(2) Manually modify the sphere file to place a space between the x and y coordinates. 

change from:
DOCK 3.5 receptor_spheres
cluster     1   number of spheres in cluster    78
  707 -33.09760-166.17085 102.97881   1.401 1901 0  0
  712 -33.89517-163.42758  96.20749   1.400 2280 0  0
 1121 -41.28802-160.96045 101.66316   1.400 1759 0  0
 1131 -38.10195-158.30315 102.35743   2.409 1916 0  0
 1132 -38.40201-156.86279 100.07462   1.401 1744 0  0
 1152 -35.59296-155.01543  95.68601   1.401 2241 0  0
 1169 -35.01744-154.05220  94.01767   1.401 2241 0  0
 1377 -30.56226-162.93300 104.71400   3.966  708 0  0

To:
DOCK 3.5 receptor_spheres
cluster     1   number of spheres in cluster    78
  707 -33.0976 -166.17085 102.97881   1.401 1901 0  0
  712 -33.8951 -163.42758  96.20749   1.400 2280 0  0
 1121 -41.2880 -160.96045 101.66316   1.400 1759 0  0
 1131 -38.1019 -158.30315 102.35743   2.409 1916 0  0
 1132 -38.4020 -156.86279 100.07462   1.401 1744 0  0
 1152 -35.5929 -155.01543  95.68601   1.401 2241 0  0
 1169 -35.0174 -154.05220  94.01767   1.401 2241 0  0
 1377 -30.5622 -162.93300 104.71400   3.966  708 0  0

(3)  Alternatively, use a program (like chimera) to translate (use the move command) the center of mass of your protein to the origin.

I hope this helps,

Trent E. Balius
Graduate Student, Rizzo Group,
Department of Applied Mathematics and Statistics,
Stony Brook University.
Office: Math Tower 3-129, Phone: (631) 632-8519
URL: http://www.ams.sunysb.edu/~tbalius/

 

 

-----Original Message-----
From: Benny Lo <benny_yc_lo at yahoo.com>
To: Trent E. Balius <tbalius at aol.com>
Sent: Wed, Jun 22, 2011 8:01 pm
Subject: Re: Sphere Selector Error








 



 



 



 



 
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