Autodock关于 pdbqt保存的问题

小草

我比较2，所以常常做一些很囧的事情，比如:
一次，我导入PDB加电荷merge非极性H后，直接去save write PDBQT，结果就
    Error ：Cannot create the pdbqt file, all atoms do not have an autodock -element field.
原因是没：Edit->Atoms->Assign AD4 {:soso_e110:}
好吧，其实通常是去水加H后直接Grid（或里ligand）->Macromolecule->Choose（这一步完成adding gasteiger charges, merging non-polar hydrogens, adding autodock_elements
and opening a file browser for you to select  a filename for writing the pdbqt.

另，ADL的一个Q&A，附上：

Hi Lisa,

usually this means that there is no partial charge on that specific atom.

One solution could be to calculate the partial charges in a different way by using
semi-empirical or QM packages (MOPAC, Gaussian, Gamess...), save the molecule as Mol2 and
use the prepare_ligand4.py script (that comes with ADT) with the "-C" or "-p" options to
preserve all the charges or only the one in your atom type, respectively.

Another solution could be to edit the PDBQT ligand file and manually add a "reasonable"
charge, while keeping the total molecular charge as integer (0.0, +1.0, -2.0, ...)

Hope this helps,

Stefano



Lisa Brown wrote:
> Hi all,
> I got the follwing massage when I tried to creat pdbqt file for a ligand.
>
> "Sorry, there are no Gasteiger parameters available for atom
> lig.1010:X :     O:O "
>
> Does any one know how to solve this.
> Any suggestions are highly appreciated.
> Thank you in advance
> LB
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
...[show rest of quote]


--
  Stefano Forli, PhD

  Research Associate
  Olson Molecular Graphics Laboratory
  Dept. Molecular Biology,  MB-5
  The Scripps Research Institute
  10550  North Torrey Pines Road