Subject: Dock4.0 + InsightII, charge, orientaion tried 0

From: "Jianhui Wu" <[email-masked]>
Date: Mon, 14 Feb 2000 17:44:07 -0500

Dear all,

(1). Assigning charges using insightII

I am using DOCK 4.0.1. Unfortunately, I have to use InsightII
instead of Sybyl to assign charges for ligands. My question is
what forcefield is more suitable for DOCK 4.0.1?

The receptor is assigned with Amber charge. However, it is
very difficult to assign Amber charge for a large database
(organic compounds) automatically. Therefore, I try to use
CVFF (consistent-valence forcefield). The docking result is
reasonable. However, I do not like the idea to mix two forcefield
in one calculation. (CVFF charge and Amber charge are derived
quite differently). At second thoughts, I might just go on doing it
as far as the result is good. But I am really not sure about it. Any
suggestion would be greatly appreciated.

By the way, regarding Gasteiger charges computed by Sybyl, is
there freeware that can produce similar charges at similar speed?

(2). Orientation tried   0, Orientation score 0, why?

Again, it is DOCK 4.0.1.  When I dock a single ligand,
I get a message that 0 orientation was tried and 0 orientation
was scored (in fact, it happens a dozens times to me now).
Yes, the ligand is small related to the binding site defined.
I thought this is the reason for that until I encounter an even
smaller molecule which DOCK processed it and scored it. How come
DOCK kick that first molecule out without even try one orientaion?
(The structure is correct. The min & max heavy atoms are correctly set).

Thanks a lot for your help.

Regards,

Jian Hui Wu
email:  [email-masked]