ADL: problem with DNA

Maria Letizia Barreca barreca at pharma.unime.it
Wed Sep 29 08:56:16 PDT 2004


Dear Autodock community,
I would like to use AutoDockTools to dock ligands into DNA-protein-Mg
complex. 

I have thus prepared the complex.pdbqs file using ADT , providing energy
coefficients for the phosphorus atom (atom type X) and Mg (atom type M).

 

However, I have noticed that no charges and solvation values were add to the
DNA (please find below one base as example)

 

ATOM   5282  X   A   C   2     -34.487  35.405 -40.484  1.00  0.00     0.000
0.00    0.00

ATOM   5283  O1P A   C   2     -35.751  35.261 -39.735  1.00  0.00     0.000
0.00    0.00

ATOM   5284  O2P A   C   2     -33.529  36.405 -39.951  1.00  0.00     0.000
0.00    0.00

ATOM   5285  O5* A   C   2     -33.761  33.990 -40.606  1.00  0.00     0.000
0.00    0.00

ATOM   5286  C5* A   C   2     -34.355  32.973 -41.451  1.00  0.00     0.000
0.00    0.00

ATOM   5287  C4* A   C   2     -34.107  31.606 -40.856  1.00  0.00     0.000
0.00    0.00

ATOM   5288  O4* A   C   2     -32.753  31.180 -41.213  1.00  0.00     0.000
0.00    0.00

ATOM   5289  C3* A   C   2     -34.142  31.512 -39.332  1.00  0.00     0.000
0.00    0.00

ATOM   5290  O3* A   C   2     -34.436  30.194 -38.880  1.00  0.00     0.000
0.00    0.00

ATOM   5291  C2* A   C   2     -32.718  31.870 -38.939  1.00  0.00     0.000
0.00    0.00

ATOM   5292  C1* A   C   2     -31.911  31.263 -40.080  1.00  0.00     0.000
0.00    0.00

ATOM   5293  N9  A   C   2     -30.716  32.064 -40.460  1.00  0.00     0.000
0.00    0.00

ATOM   5294  C8  A   C   2     -30.587  33.425 -40.507  1.00  0.00     0.000
0.00    0.00

ATOM   5295  N7  A   C   2     -29.410  33.824 -40.886  1.00  0.00     0.000
0.00    0.00

ATOM   5296  H7  A   C   2     -29.078  34.781 -41.005  1.00  0.00     0.000
0.00    0.00

ATOM   5297  C5  A   C   2     -28.712  32.647 -41.091  1.00  0.00     0.000
0.00    0.00

ATOM   5298  C6  A   C   2     -27.390  32.385 -41.510  1.00  0.00     0.000
0.00    0.00

ATOM   5299  N6  A   C   2     -26.506  33.355 -41.795  1.00  0.00     0.000
0.00    0.00

ATOM   5300  H61 A   C   2     -25.551  33.166 -42.098  1.00  0.00     0.000
0.00    0.00

ATOM   5301  H62 A   C   2     -26.787  34.332 -41.711  1.00  0.00     0.000
0.00    0.00

ATOM   5302  N1  A   C   2     -27.020  31.101 -41.620  1.00  0.00     0.000
0.00    0.00

ATOM   5303  H1  A   C   2     -26.076  30.857 -41.919  1.00  0.00     0.000
0.00    0.00

ATOM   5304  C2  A   C   2     -27.904  30.151 -41.333  1.00  0.00     0.000
0.00    0.00

ATOM   5305  N3  A   C   2     -29.156  30.262 -40.942  1.00  0.00     0.000
0.00    0.00

ATOM   5306  H3  A   C   2     -29.777  29.478 -40.742  1.00  0.00     0.000
0.00    0.00

 

 

Moreover, the partial charge of the Mg ion is set to zero by ADT  (I have
inserted 1.30 and 0.875 for R(ij) and eps(ij) , respectively)

 

HETATM 5261  M   MG  B 271      10.933  10.884  25.412  1.00  0.00     0.000
0.00    0.00

HETATM 5262  M   MG  B 272      12.849   7.534  25.617  1.00  0.00     0.000
0.00    0.00

 

Do I have manually to edit the pdbqs file and replace the 0.00 charge by
2.0? 

 

Thanks a lot for any help anyone can give!

 

Letizia

 

 

-------------------------------------------------------------------------

Maria Letizia Barreca, Ph.D.

Dipartimento Farmaco-Chimico

Universita'degli Studi di Messina

Viale Annunziata 98168 MESSINA ITALY

Phone: +39 090 6766464

Fax:   +39 090 355613

email: barrecal at pharma.unime

 




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