[gmx-users] Re: Protein ligand simulation

Justin A. Lemkul jalemkul at vt.edu
Fri Dec 2 03:24:46 CET 2011



bharat gupta wrote:
> Here's the coordinate of the phosphate ion from the docked complex :-
> ATOM   2209  N   GLY A 228      -4.491  73.252   3.100  1.00 31.50   
>  -0.336 N 
> ATOM   2210  HN  GLY A 228      -4.765  72.618   3.850  1.00  0.00     
> 0.164 HD
> ATOM   2211  CA  GLY A 228      -4.817  74.668   3.205  1.00 34.50     
> 0.189 C 
> ATOM   2212  C   GLY A 228      -6.283  75.040   3.026  1.00 36.60     
> 0.253 C 
> ATOM   2213  O   GLY A 228      -6.638  76.216   3.151  1.00 36.80   
>  -0.270 OA
> ATOM   2214  N   ILE A 229      -7.109  74.064   2.647  1.00 38.60   
>  -0.337 N 
> ATOM   2215  HN  ILE A 229      -6.718  73.136   2.484  1.00  0.00     
> 0.164 HD
> ATOM   2216  CA  ILE A 229      -8.556  74.256   2.452  1.00 41.10     
> 0.159 C 
> ATOM   2217  C   ILE A 229      -9.275  73.368   3.447  1.00 43.10     
> 0.251 C 
> ATOM   2218  O   ILE A 229      -8.856  72.229   3.655  1.00 43.60   
>  -0.271 OA
> ATOM   2219  CB  ILE A 229      -9.003  73.826   1.031  1.00 40.40     
> 0.029 C 
> ATOM   2220  CG1 ILE A 229      -8.528  74.844   0.013  1.00 40.50     
> 0.002 C 
> ATOM   2221  CG2 ILE A 229     -10.512  73.689   0.942  1.00 39.90     
> 0.002 C 
> ATOM   2222  CD1 ILE A 229      -8.610  74.327  -1.389  1.00 41.40     
> 0.000 C 
> ATOM   2223  N   THR A 230     -10.312  73.894   4.098  1.00 45.60   
>  -0.337 N 
> ATOM   2224  HN  THR A 230     -10.544  74.877   3.957  1.00  0.00     
> 0.164 HD
> ATOM   2225  CA  THR A 230     -11.129  73.085   5.017  1.00 47.90     
> 0.172 C 
> ATOM   2226  C   THR A 230     -12.555  72.789   4.490  1.00 49.10     
> 0.232 C 
> ATOM   2227  O   THR A 230     -12.945  71.602   4.523  1.00 50.90   
>  -0.286 OA
> ATOM   2228  CB  THR A 230     -11.179  73.714   6.460  1.00 48.20     
> 0.139 C 
> ATOM   2229  OG1 THR A 230     -11.348  75.136   6.384  1.00 48.60   
>  -0.383 OA
> ATOM   2230  HG1 THR A 230     -12.152  75.322   5.914  1.00  0.00     
> 0.210 HD
> ATOM   2231  CG2 THR A 230      -9.880  73.414   7.220  1.00 49.10     
> 0.034 C 
> TER    2232      THR A 230 
> HETATM    1  P   PO4 A 322      28.148  82.525   1.696  1.00  2.95     
> 0.437 P 
> HETATM    2  O1  PO4 A 322      27.246  83.314   2.595  1.00  5.93   
>  -0.609 OA
> HETATM    3  O2  PO4 A 322      27.419  81.238   1.254  1.00  4.49   
>  -0.609 OA
> HETATM    4  O3  PO4 A 322      28.535  83.301   0.471  1.00  2.00   
>  -0.609 OA
> HETATM    5  O4  PO4 A 322      29.451  82.186   2.489  1.00  4.00   
>  -0.609 OA
> 
> 
> 
> Here's the coordinates of the processed file after adding ligand 
> coordinates :-
> 
> 
>  230THR      N 3601  -1.031   7.389   0.410
>   230THR     HN 3602  -1.054   7.486   0.396
>   230THR     CA 3603  -1.113   7.308   0.502
>   230THR     HA 3604  -1.063   7.222   0.502
>   230THR     CB 3605  -1.118   7.371   0.646
>   230THR     HB 3606  -1.197   7.338   0.697
>   230THR    OG1 3607  -1.135   7.514   0.638
>   230THR    HG1 3608  -1.138   7.552   0.731
>   230THR    CG2 3609  -0.988   7.341   0.722
>   230THR   HG21 3610  -0.993   7.382   0.813
>   230THR   HG22 3611  -0.976   7.242   0.730
>   230THR   HG23 3612  -0.910   7.380   0.672
>   230THR      C 3613  -1.255   7.279   0.449
>   230THR    OT1 3614  -1.294   7.160   0.452
>   230THR    OT2 3615  -1.337   7.205   0.529
>     1LIG   P       1  28.261  82.425   1.961   
>     1LIG  O1       2  27.805  80.999   1.894   
>     1LIG  O2       3  28.523  82.938   0.528   
>     1LIG  O3       4  27.235  83.311   2.606   
>     1LIG  O4       5  29.563  82.481   2.823
>    5.23907   4.16174   3.66560
> 

Your PO4 coordinates are still in Angstrom.  They should be nm for a .gro file.

-Justin

> 
> On Fri, Dec 2, 2011 at 11:18 AM, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> wrote:
> 
> 
> 
>     bharat gupta wrote:
> 
>         I checked the docked structure and the structure obtained after
>         adding the ligand coordinates to the processed file obtained
>         after using pdb2gmx command. It's very surprising that in the
>         docked structure ligand is at the correct place but the
>         processed gromacs file the ligand lies far apart from the
>         protein. Any clue what could be the reason for this ??
> 
> 
>     If the docked structure is correct, and the one you reassembled is
>     incorrect, you made some mistake in putting it back together.  It's
>     impossible to say what went wrong based on the (lack of) information
>     given.
> 
>     -Justin
> 
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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> 
> -- 
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================



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