The Molecular Graphics Laboratory Forum

Thanks for the help with the division error problem. Babel in fact converted some of the molecules when I got the options right, but failed after converting less than 10% of the file. With your guidance the problem was solved by using ChemAxon molconvert to generate 3D structures with hydrogens attached. The file looks fine and displays properly (mview or PMV).
Next problem. A subset of the compounds contain a silicon atom. When adding the molecules into RACCOON, those molecules with silicon atoms give the error message that no gasteiger parameters are available for Si1. Is there a way to add or calculate the parameter, or is the easiest path to just remove those compounds from the screening set?

Thanks again,
Dick

Dick,

The error message you see is from the underlying AutoDock tools that cannot find the parameters for assignign the partial charges.
Although, the Si atom type is not present in the AutoDock forcefield either.
Raccoon supports only AutoDock atom types, then to avoid errors later during the calculation, these ligands are also filtered out automatically (see the filtering options). So in theory if you keep preparing your virtual screening, these ligands shouldn't be included.

The choices you have are the following:
- try to find some suitable parameters to be included in the forcefield (then you also manually fix partial charges in these ligands);

- modify the Si types to become the closest atom yype already present in the forcefield (i.e. C?) and hope that there is no direct and specific interaction between the Si atom and the receptor structure (that would be treated as a carbon interaction);

- ignore these ligands.

Hope this helps,

Stefano