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From: "Christian Buning" <Christian.Buning@gmd.de>

Cc: <yuntang@ncifcrf.gov>

Sent: Tuesday, October 02, 2001 11:22 AM

Subject: Re: Ask for a dock program

Dear Yun,

I would like to correct the info you gave = in your=20 request. FlexX is in fact able to consider both
metal ions and = DNA as=20 part of the active site, so it might be a good choice for your=20 problem.

=20 Christian
------------------------------------------------------------= ------------
Dr.=20 Christian=20 Buning
&nb= sp; =20
Fraunhofer-Institute for Algorithms and Scientific Computing=20 (SCAI)
Schloss Birlinghoven
D-53754 Sankt Augustin

Tel: +49 = - 2241=20 - 14 - 2997
Fax: +49 - 2241 - 14 - 2656
E-mail: Christian.Buning@scai= .fraunhofer.de
Internet:=20 http://www.scai.fraunhofer.de=
---------------------------------------------------------------------= ---

From: "Oliver Hucke" <hucke@uni-freiburg.de>

To: <chemistry@ccl.net>;=20 <yuntang@ncifcrf.gov>

Sent: Tuesday, October 02, 2001 12:16 PM

Subject: Re: Ask for a dock program

Dear Yun,

we use FlexX for ligand docking = calculations. With=20 this program, you can
include non protein structures as part
of = the=20 receptor. I have done so with Chlorophylls and Pheophytines and
it = should be=20 possible with DNA as well, if you include it as
hetero-file in = the rdf=20 file (you have to convert your dna to the mol2
format for this = purpose - this=20 is documented in the manual in the
section about the receptor = description=20 file).
We also had the problem with the inclusion of mg. It could be = solved=20 by
the inclusion of the following lines in the amino.dat=20 file
(~/flex/static_data/ dircectory):

@template=20 _mg
atom mg
iact mg - - - metal=20 metal_sp

The MG in our pdb file was named MG2, so that we = had to=20 add the
following line to the @templates section of our receptor=20 description
file:

MG2 * * _mg

Hope this helps. = Let me=20 know if you have further questions.

Kind = regards,

=20 Oliver
______________________________________

= Oliver=20 Hucke
Inst. fuer Physikalische Chemie II
Universitaet=20 Freiburg
Albertstr. 23a
D-79104 Freiburg

= Tel.=20 : +49-761-203-5130 (/-6179)
Fax. : =20 +49-761-203-6189
email: hucke@uni-freiburg.de
= ______________________________________

From: "Garrett M. Morris" <garrett@scripps.edu>

To: "Yun Tang" <yuntang@ncifcrf.gov>

Cc: "Garrett M. Morris" <garrett@scripps.edu>

Sent: Tuesday, October 02, 2001 2:36 PM

Subject: Re: CCL:Ask for a dock program

Dear Yun,

On Mon, 1 Oct 2001, Yun Tang = wrote:

=20 This is not correct for AutoDock: AutoDock can calculate maps for=20 all
the atoms in DNA and for Mg2+. You can define the Mg2+ = using=20 the
r-eqm and epsilon (well depth) parameters, and set the = partial
charge=20 to +2. See the AutoDock home page and click on the
"Parameters" = link.

Good luck, and happy docking!

Best=20 wishes,

Garrett
___
Dr Garrett M. Morris, MA,=20 DPhil
The Scripps Research=20 Institute,       tel: (858)=20 784-2292
Dept. Molecular Biology, =20 MB-5,       fax: (858)=20 784-2860
10550 North Torrey Pines=20 Road,       email: garrett@scripps.edu
La=20 Jolla, CA 92037-1000, = USA.       www.scripps.edu/pub/ols= on-web/gmm

From: "Ng Pei Ling" <ngpeiling1@yahoo.com>

To: "Yun Tang" <yuntang@ncifcrf.gov>

Sent: Tuesday, October 02, 2001 9:20 PM

Subject: Re: CCL:Ask for a dock program

To Yun Tang :
I. m a master student in = Phamarceutical=20 Science
USM, Penang. Nice to know you. I have same experience
with = you. I=20 used small molecule of flavonoids from
plants dock with enzyme = cancer. I 'm=20 trying to assign
the charges before using docking programe. I = advice
you=20 to read the "manual of Dock User" properly before
docking. Hope can = keep in=20 touch and exchange
experience with you.

From: "Bruno Sopko" <b_sopko@yahoo.com>

To: "Yun Tang" <yuntang@ncifcrf.gov>

Sent: Thursday, October 04, 2001 2:49 AM

Subject: Re: CCL:Ask for a dock program

It is possible to use the Autodock programm, however,
you have = to change=20 the HETATM charges and solvation
parameters in the pdbqs file MANUALY = (the=20 charges can
be taken from the mol2 file, but the = solvation
parameters are=20 the MUST).
One hint - look in the addsol source code and = choose
the most=20 resembling parameters.
Good luck
Bruno = Sopko