ADL: Autodock tools atom type

Saha, Rinku SahaRinku at uams.edu
Thu Jun 20 04:20:38 PDT 2013


Hi
I have a .pdb file which has a ligand included in it. I then minimized this .pdb file in Sybyl .
Now I needed to convert this minimized .pdb file(with a ligand included in it called NAD) to .pdbqt using Autodock. To do so I had to remove the lp atoms manually and change the HETATM to ATOM(as shown in the lines below:

ATOM   1038 LPD1 MET C  76     -13.926   1.062 -24.367  1.00  0.00          LP
ATOM   1039 LPD2 MET C  76     -14.782   0.368 -24.488  1.00  0.00          LP
ATOM   1604 LPG1 CYS C 110     -19.889  -7.989 -23.643  1.00  0.00          LP
ATOM   1605 LPG2 CYS C 110     -20.173  -7.382 -24.526  1.00  0.00          LP

HETATM17190  H2N NAD A 602     -13.118  10.640  -1.397  1.00  0.00           H
HETATM17191  C3N NAD A 602     -11.785  12.054  -2.365  1.00 37.92           C
HETATM17192  C7N NAD A 602     -10.617  11.044  -2.506  1.00 35.87           C
HETATM17193  O7N NAD A 602     -10.723   9.889  -2.091  1.00 34.20           O
HETATM17194  N7N NAD A 602      -9.516  11.516  -3.094  1.00 33.96           N
HETATM17195 H72N NAD A 602      -9.485  12.464  -3.409  1.00  0.00           H
HETATM17196 H71N NAD A 602      -8.722  10.921  -3.219  1.00  0.00           H
HETATM17197  C4N NAD A 602     -11.646  13.387  -2.854  1.00 38.37           C
HETATM17198  H4N NAD A 602     -10.718  13.689  -3.326  1.00  0.00           H
HETATM17199  C5N NAD A 602     -12.705  14.323  -2.732  1.00 39.60           C
HETATM17200  H5N NAD A 602     -12.581  15.334  -3.102  1.00  0.00           H
HETATM17201  C6N NAD A 602     -13.919  13.936  -2.129  1.00 42.79           C
HETATM17202  H6N NAD A 602     -14.731  14.649  -2.041  1.00  0.00           H

The Autodock tools gave a .pdbqt file but when I use it to dock there is a error saying "not able to recognize atom type Ho.(as shown in few lines below)
ATOM   5230 HO3N NAD A 601     -34.496  -6.753 -27.979  1.00  0.00     0.251 Ho
ATOM   5231  O2D NAD A 601     -33.751  -4.924 -26.736  1.00 29.73     0.000 OA
ATOM   5232 HO2N NAD A 601     -33.290  -4.171 -26.385  1.00  0.00     0.168 Ho
ATOM   5233  N1N NAD A 601     -35.603  -2.957 -25.046  1.00 22.41    -0.347 N


Will greatly appreciate any helpful suggestion.
Best
saha
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