ADL: Partial charges and a route to MD

Francesco Pietra chiendarret at yahoo.com
Sun May 4 02:43:51 PDT 2008


New to autodock, coming from some non-commercial experience (to appear soon in the literature) with MD and other docking programs.

I was rather surprised seeing that Gasteiger partial charges are used for non standard residues with ADT. Searching on the archives, I came across

Jeffrey Dyason j.dyason at griffith.edu.au
Tue Apr 27 15:27:06 PDT 2004

as the post probably most close to my problems. Is anything new about the type of partial charges used in ADT/autodock4 that I may have missed?

If I understand, the use of Gasteiger partial charges implies that approximations in docking simulations are so large that it is not worth while to use more modern partial charges. At any event, is there any way with ADT to use AM1 or RESP calculated partial charges? This question implies that I am along an atypical route: I am not interested in comparing a huge number of ligands, rather simulating docking of a very small number of (large and flexible) ligands. Also, I wish is to simulate (with MD) what happens later when the built complex is immersed in an as-much-as-possible realistic situation. Let me exemplify in a double layer lipidic membrane for proteins that I know are stabilized by the membrane, while they tend to undergo deformation in a vacuum or even implicit solvation. Therefore, where to find info how to use the complex coming from autodock with MD simulations (I mean Amber in the first instance)? Is it any program for name/type conversion
 of atoms and so on? I already had to spend much time in getting Amber9 and Chimera to understand each other to this regard.

Thanks
francesco pietra


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