Autodock关于 pdbqt保存的问题
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 selecta 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
10550North Torrey Pines Road
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