From chemistry-request@server.ccl.net Sat Mar  1 13:01:34 2003
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Date: Sat, 01 Mar 2003 21:30:28 +0330
To: CHEMISTRY@ccl.net
From: "Armin M. Sobhani" <armin@iums.ac.ir>
Subject: Re: CCL:Database screening with Autodock
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Dear Marco,

I've succeeded in compiling AutoDock 3.0.5 under Windows 9x/Me/NT/2000/XP. 
It only consists of three main executive programs (i.e. autotors, autogrid 
and autodock). It lacks all unix shell and awk scripts and that's why I am 
working on a graphical front-end for it (named WAD, i.e. Windows AutoDock) 
using MFC and Visual C++. In this front-end you can specify several ligand 
molecules in HyperChem7 HIN format as input. It's possible to implement 
other file formats in the future. In my rough estimate the first working 
release would be ready in a two-week period. If you are interested, I will 
let you know when it's ready.

Cheers,

Armin

At 11:25 Þ.Ù 2003/02/28 +0100, you wrote:
>my question is about database screening with AUTODOCK3.0.5;
>If possible i would like to screen entire ACD database with autodock, but i'm
>still looking for someone who did it...
>I know there is no  a "standard" method to do this, but i think it's possible
>with some shell scripts...
>Have you some information about this question?

p-----__---_________----____----------------------------------------q
|    /  \ /  _   _  \  / ____\ Armin M. Sobhani, PharmD, PhD        |
|   /    \\  \\  \\  \/\ \___/_ Assitant Prof., Pharmacology Dept.  |
|  /  /\  \\  \\  \\  \ \_____ \ Iran University of Medical Sciences|
| (   ___  \\  \\  \\  \/____/\ \ mailto:armin@iums.ac.ir           |
|( \__\_/\__\\__\\__\\__\/\_____/ Tel: +98 (21) 805 2265, Fax: ~64  |
| \/__/ \/__//__//__//__/\/____/ P.O.Box: 14155-6183, Tehran, IRAN  |
|~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
|  Once you understand the universe at the atomic level everything  |
|  else is easy.                               -Richard P. Feynman  |
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From chemistry-request@server.ccl.net Sat Mar  1 12:28:22 2003
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From: =?iso-8859-1?q?Michele=20Lunelli?= <efunit@yahoo.it>
Subject: Format and units of Hessian in Gaussian
To: CHEMISTRY@ccl.net
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Hi,
I performed a frequency calculation in g98 to obtain
the second derivatives matrix. I found the values in
the (formatted) checkpoint file, but I'm not sure
about the order of the values in the file. The matrix
is symmetric, so only a (lower?) triangle of elements
are reported. If, for example, I have the water
molecules with the atoms at this coordinates:
O (x1,y1,z1)
H (x2,y2,z2)
H (x3,y3,z3)
and indicating the matrix elements U(a,b) as the
second derivative of the eneregy with respect to the
coordinates a and b, how are the values ordered in the
fchk file? Is this correct:
U(x1,x1) U(y1,x1) U(y1,y1) U(z1,x1) U(z1,y1) U(z1,z1)
U(x2,x1) U(x2,y1) ...

And are the values expressend in atomic units
hartree/(bohr^2)?

Regards,
Michele Lunelli
University of Trento
Italy


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