[Dock-fans] query on dock results

Trent Balius tbalius at aol.com
Thu Mar 4 07:10:10 PST 2010


 
Mol2 files, like pdb files, specify the 3D coordinates of a molecule.  

DOCK outputs a mol2 file.  This file can be visualized with a program such as UCSF Chimera.
    
See the manual for more information on mol2 files:
    
http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#TriposMOL2Format
  
 
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

 

 

-----Original Message-----
From: ethel urzo <reau_05 at yahoo.com>
To: dock-fans at mailman.docking.org
Sent: Wed, Feb 10, 2010 11:02 pm
Subject: [Dock-fans] query on dock results




Dear everyone,

When I opened the rigid & flexible docking output files in Notepad, I saw the ff: texts:


@<TRIPOS>MOLECULE
AT1.pdb
 28 31 1 0 0
SMALL
AMBER ff03.r1


@<TRIPOS>ATOM
      1 C          91.5041   29.5620   17.1702 C.2     1  1           0.0241
      2 C          92.2978   30.7051   16.9774 C.2     1  2          -0.2090
      3 C          92.7050   31.4429   18.1063 C.2     1  3          -0.0973
      4 C          92.3123   31.0234   19.3862 C.2     1  4          -0.1925
      5 C          91.5275   29.8812   19.4937 C.2     1  5          -0.0344
      6 N          91.1355   29.1705   18.4035 N.pl3   1  6          -0.2572
      7 C          92.6995   31.1248   15.6192 C.2     1  7           0.7468
      8 N          93.5090   32.3047   15.5797 N.pl3   1  8          -0.2478
      9 N          93.5087   32.6067   17.9769 N.pl3   1  9           0.0090
     10 C          93.8751   32.9913   16.7875 C.2     1  10         -0.2613
     11 C          94.0930   33.0045   14.4568 C.2     1  11          0.1024
     12 C          94.8181   34.1227   14.9327 C.2     1  12         -0.1764
     13 C          94.7302   34.1908   16.4161 C.2     1  13          0.3422
     14 O          92.4040   30.5661   14.5767 O.2     1  14         -0.6346
     15 O          95.2176   35.0002   17.1642 O.2     1  15         -0.3524
     16 C          94.0206   32.7174   13.1023 C.2     1  16         -0.1579
     17 C          94.6921   33.5746   12.2244 C.2     1  17         -0.0857
     18 C          95.4048   34.6745   12.6848 C.2     1  18         -0.1775
     19 C          95.4745   34.9609   14.0514 C.2     1  19         -0.0415
     20 H          91.1842   28.9874   16.3135 H       1  1           0.1844
     21 H          92.6122   31.5739   20.2656 H       1  4           0.1516
     22 H          91.2197   29.5481   20.4738 H       1  5           0.1586
     23 H          90.5651   28.3451   18.5197 H       1  6           0.3037
     24 H          93.7917   33.1280   18.7943 H       1  9           0.3245
     25 H          96.0278   35.8163   14.4098 H       1  19          0.1480
     26 H          95.9111   35.3160   11.9787 H       1  18          0.1337
     27 H          94.6557   33.3767   11.1633 H       1  17          0.1325
     28 H          93.4668   31.8643   12.7388 H       1  16          0.1642

Can anybody tell me what are these and where can I use these?
Thanks.

Rea Ethel Urzo
BS Cemistry Student
University of the Philippines




      
  Get your new Email address!  
Grab the Email name you've always wanted before someone else does!
 
_______________________________________________
Dock-fans mailing list
Dock-fans at mailman.docking.org
http://mailman.docking.org/mailman/listinfo/dock-fans

 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mailman.docking.org/pipermail/dock-fans/attachments/20100304/cdb9a24e/attachment.html 


More information about the Dock-fans mailing list