ADL: New atom types in parameter file

Sharath Roy royshari87 at yahoo.in
Tue Apr 21 23:03:42 PDT 2009


Hi ..........

In a docking program, I found the dlg not to be found for certain entries because of having extra atom types in ligand-pdbqt......the extra types are As, Cu, Sb and so on.........
So, this has to be added in the AD4_parameters.dat..........

My question is we shud also provide with the Rii , solpar, rec_index etc..........parameters ...........So hw is this accomplished???

When I use the prepare_ligand4.py script for preparing the lig, it shows a warning so as to Gastegier charges cannot be computed for the extra atom types..........But i did it in ADT, and it assigned zero charge for those extra atoms............

But it s taken into problematic consideration in autodock -step..........

How to proceed??

Thanx in advance



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