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From: "michael hanlon (BITS)" <michael.hanlon@bbsrc.ac.uk>
To: "'chemistry@ccl.net'" <chemistry@ccl.net>
Subject: molecular docking startup
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Hello all,

I would be very grateful for pointers/advise etc on
software/reviews/literature suitable for a newcomer to molecular docking
(protein/protein/, protein/ligand).

Thanks,
Mike

Dr. Mike Hanlon
Molecular Biology Computing Support
BBSRC Bioscience IT Services
West Common
Harpenden
Herts AL5 2JE 
Phone: 01582 714904
Email: molbio.support@bbsrc.ac.uk
Web: http://www.molbiol.bbsrc.ac.uk 
 

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Subject: About freezing coordinates in opt 
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Dear Sir,

I now use the Gaussian98 to opt large systems,and I want to freeze some variables. Would you kindly tell me how to do?(give an example: such as H2O) Thanks.

Yi Gao
Nanjing Univ. P.R.China


______________________________________

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From chemistry-request@server.ccl.net Sun Feb 24 13:59:51 2002
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    Hi,

        Is a dual processor Athlon more efficient than two single
processors? Does somebody do a benchmark for measure the efficiency of
dual boards like ASUS A7M 266-D or MSI K7D ?

    Thanks,

        Alexander.

--
***************************************************************************
 Alexander Martins da Silva           emails: alex.msilva@uol.com.br
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 Dept. de F韘ico-Qu韒ica              Phone:  +55-21-2562-7179 (office)
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From chemistry-request@server.ccl.net Mon Feb 25 03:54:31 2002
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From: Christian.Pilger@bc.boehringer-ingelheim.com
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Subject: aqueous solubilities - summary part 2
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> Dear colleagues,
> 
> I received two more replies to my inquiry on the prediction of aqueous
> solubilities:
> 
> Pieter Stouten [pieter.stouten@pharmacia.com] has made available a series
> of very informative slides, that can be downloaded from
> http://www.shogi.net/solubility/
> 
> Wayne Steinmetz [WES04747@pomona.edu] suggests the following:
> 
>  I intended to respond to your request earlier but fell behind in my other
> work.  I spent my third sabbatical leave at Abbott Laboratories with the
> goal of learning modeling techniques.  This included CoMFA.  As a vehicle
> for mastering CoMFA, I developed a model for the solubility of amino acids
> in water.  The work is reported in Quant. Struct.-Act. Relat.,
> 14, 14-23 (1995).  A great deal of time was invested in the calculations.
> Automating the procedure would be challenging.  I agree with one of the
> respondents.  Solubility depends on a number of factors including the
> crystallographic space group of the solid solute.  I'm not confident that
> one model can accommodate all the variables.
> 
> 
> Again, thank you very much !
> 
> Best regards,
> 
> Christian
> ________________________________________________________________
> 
>    Dr. Christian Pilger
>    Dept. Chemical Research / Structural Research
>    K91-00-10
>    Boehringer Ingelheim Pharma KG
>    D-88397 Biberach/Germany
>    Phone: 07351-545749
>    Fax:     07351-5497924
>    mailto: christian.pilger@bc.boehringer-ingelheim.com
> 


From chemistry-request@server.ccl.net Mon Feb 25 05:13:38 2002
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Date: Mon, 25 Feb 2002 11:13:11 +0100 (MET)
From: Andreas Goetz <Andreas.Goetz@chemie.uni-erlangen.de>
To: Eric Brown <ecbrown@u.washington.edu>
Cc: <chemistry@ccl.net>
Subject: Re: CCL:Gaussian Molecular Integrals
In-Reply-To: <B89D7725.18C1%ecbrown@u.washington.edu>
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Hi,

the following book contains a good chapter about molecular integral
evaluation:

 Helgaker, Jorgensen, Olsen: Molecular Electronic-Structure Theory;
 John Wiley & Sons, 2000.


Greetings,
	Andreas

On Sat, 23 Feb 2002, Eric Brown wrote:

> Dear CCLers,
>
>     I wish to write a small Mathematica program which is able to evaluate
> all the integrals (over gaussian-type orbitals) required in a Hartree-Fock
> calculation. Having checked a number of online resources (Fermann in the
> Book of Knowledge, et al.) and text books (Szabo and Ostlund, et al.), I
> have noticed that many of their formulae are incomplete with respect to what
> I wish to calculate:
>
> A) arbitrary angular momentum
> B) x, y, and z instead of r
> C) notations immediately understandable by this organic chemist
>    (Sums and error functions are fine)
> D) when normalizations should be performed
> E) S, T, V, ERI
> F) perhaps their derivatives (but this is a later step)
>
>     In general, I have been able to find many works which demonstrate
> integral calculations for 1s functions. Since these integral calculations
> have been implemented in many ab initio programs, I thought that it would be
> easy to find these spelled out.
>
>     Any pointers or solutions would be -most- welcomed!
>
> Wishing you the best,
>
> Eric Brown
> University of Washington
>
>
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
> MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
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>
>
>
>
>
>

_________________________________________________________________
                                            Theoretische Chemie,
Andreas Goetz                               Universitaet Erlangen
                                            Egerlandstr. 3
                                            D-91058 Erlangen
Tel.   : +49-9131-8527772
Fax    : +49-9131-8527736
e-mail : Andreas.Goetz@chemie.uni-erlangen.de
_________________________________________________________________





From chemistry-request@server.ccl.net Mon Feb 25 08:16:14 2002
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Hello there,

In my own experience of Docking packages I have found GOLD (Gareth Jones
1997) to be the most a) user friendly and b) reliable - so I would
recommend that you start here. However, it has limitations - and if you
are looking to dock largely hydrophobic ligands into hydrophobic
structures it probably will frustrate you......saying that so will a lot
of the other packages out there.

Hope this helps

Best Wishes

Stewart Kirton

-------------------------------------------------------------------------------
Stewart Kirton				|e-mail: sbk1@le.ac.uk
Dept. Chemistry				|
University of Leicester			|
University Road				|
Leicester				|
LE1 7RH					|
Tel: (0116) 2523620			|
-------------------------------------------------------------------------------


From chemistry-request@server.ccl.net Mon Feb 25 09:04:40 2002
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Date: Mon, 25 Feb 2002 09:02:27 -0500
From: "Shobe, Dave" <dshobe@sud-chemieinc.com>
Subject: RE: Cheminformatics
To: "'CCL'" <chemistry@ccl.net>, "'CHMINF-L'" <chminf-L@listserv.indiana.edu>
Message-id: 
 <157A51F55AAAD3119CD70008C7B1629D01C159D9@lvlxch01.unitedcatalysts.com>
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I don't think that's what he meant... :-)
 
Does anyone know of any degree programs in the field of chemoinformatics in
Canada?
 
--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com

Don't bother flaming me: I'm behind a firewall.



-----Original Message-----
From: Dr. Guillermo A. Morales [mailto:morales@COMBICHEMLAB.COM]
Sent: Sunday, February 24, 2002 8:48 PM
To: CHMINF-L@LISTSERV.INDIANA.EDU
Subject: Re: Cheminformatics


Hi Yan,
 
There's the Chemical Computing Group, Inc ( http://www.chemcomp.com/
<http://www.chemcomp.com/>  ) that is based in Montreal, Canada.
 
There is also Advanced Chemistry Development Inc. (
<http://www.acdlabs.com/> http://www.acdlabs.com/ ) in Toronto, Canada.
 
I hope this helps.
 
Best,
 
- Guillermo.
-----
Dr. Guillermo A. Morales
Morales Consulting
E-mail: morales@combichemlab.com
Website: http://www.combichemlab.com <http://www.combichemlab.com/> 
Member of the Combi-Web Consortium: http://www.combi-web.com
<http://www.combi-web.com/> 
  

-----Original Message-----
From: CHEMICAL INFORMATION SOURCES DISCUSSION LIST [mailto:CHMINF-L@indiana.
edu]On Behalf Of leiyan
Sent: Sunday, February 24, 2002 4:34 PM
To: CHMINF-L@LISTSERV.INDIANA.EDU
Subject: Cheminformatics



I am interested in the Cheminformatics program and would like to get a 




From chemistry-request@server.ccl.net Mon Feb 25 09:38:21 2002
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Date: Mon, 25 Feb 2002 08:49:06 -0600
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From: "Anthony J. Duben" <ajduben@semovm.semo.edu>
Subject: Re: CCL:Gaussian Molecular Integrals
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If I am not mistaken, it is possible to reduce Gaussian integrals
regardless of angular momentum to integrals over 1s type orbitals.
There is an old paper in a book "Advances in Computational Physics"
by Isaiah Shavitt (c. 1962) that spells it out.  Hope this helps.

AJD

At 04:43 PM 2/23/02 -0800, Eric Brown wrote:
>Dear CCLers,
>
>     I wish to write a small Mathematica program which is able to evaluate
>all the integrals (over gaussian-type orbitals) required in a Hartree-Fock
>calculation. Having checked a number of online resources (Fermann in the
>Book of Knowledge, et al.) and text books (Szabo and Ostlund, et al.), I
>have noticed that many of their formulae are incomplete with respect to what
>I wish to calculate:
>
>A) arbitrary angular momentum
>B) x, y, and z instead of r
>C) notations immediately understandable by this organic chemist
>    (Sums and error functions are fine)
>D) when normalizations should be performed
>E) S, T, V, ERI
>F) perhaps their derivatives (but this is a later step)
>
>     In general, I have been able to find many works which demonstrate
>integral calculations for 1s functions. Since these integral calculations
>have been implemented in many ab initio programs, I thought that it would be
>easy to find these spelled out.
>
>     Any pointers or solutions would be -most- welcomed!
>
>Wishing you the best,
>
>Eric Brown
>University of Washington
>
>
>-= This is automatically added to each message by mailing script =-
>CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
>MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
>CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net 70
>Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

********************************************************
Anthony J. Duben
Professor and Chairman
Computer Science Dept., MS 5950
Southeast Missouri State University
1 University Plaza
Cape Girardeau MO 63701-4799
phone:  573-651-2194
fax:         573-651-2791
e-mail: ajduben@semovm.semo.edu
   or        c867buc@semovm.semo.edu

"Anyone can take the helm when the sea is calm."
               -- Publilius Syrus (c. 43 B.C.)

"If we knew what it was we were doing, it would not be called
  research, would it?" -- Albert Einstein


From chemistry-request@server.ccl.net Mon Feb 25 09:44:09 2002
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From: "Nick Rhodes" <N.Rhodes@sheffield.ac.uk>
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> Does anyone know of any degree programs in the field of chemoinformatics in
> Canada?

I don't know of any but there are three established masters programmes 
- Indiana, UMIST (Manchester, UK) and of course here in Sheffield.

www.shef.ac.uk/uni/academic/I-M/is/courses/pgrad/mscci/mscci.html

Nick

*****************************************************************
Nick Rhodes (Programme Development Officer, MSc Chemoinformatics), 
Computational Information Systems Research Group, 
Department of Information Studies, University of Sheffield, 
Regent Court, 211 Portobello Street, Sheffield, 
South Yorkshire, S1 4DP, United Kingdom.
-------------
Hallam Grange Lawn Tennis Club
http://www.hallamgrange.org.uk 



From chemistry-request@server.ccl.net Mon Feb 25 10:32:51 2002
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CC: chemistry@ccl.net
Subject: Re: CCL:About freezing coordinates in opt
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t218gy wrote:
> 
> Dear Sir,
> 
> I now use the Gaussian98 to opt large systems,and I want to freeze some variables. Would you kindly tell me how to do?(give an example: such as H2O) Thanks.
> 

Check out this web: http://www.gaussian.com/opt_wp.htm
and http://www.gaussian.com/00000460.htm

Good luck. huajun

> Yi Gao
> Nanjing Univ. P.R.China
> 
> ______________________________________
> 
> ===================================================================
> 新浪免费电子邮箱 (http://mail.sina.com.cn)
> 新浪分类信息：轻松订阅，量身定制,好信息来找你! (http://classad.sina.com.cn/)
> 
> -= This is automatically added to each message by mailing script =-
> CHEMISTRY@ccl.net -- To Everybody  | CHEMISTRY-REQUEST@ccl.net -- To Admins
> MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
> CHEMISTRY-SEARCH@ccl.net -- archive search    |    Gopher: gopher.ccl.net 70
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/   | Jan: jkl@ccl.net

-- 
Hua-Jun Fan
Chemistry Department
Texas A&M University
3255 TAMU
College Station, TX 77843-3255


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From: "Mark Thompson" <mark@planaria-software.com>
To: "Andreas Goetz" <Andreas.Goetz@chemie.uni-erlangen.de>,
   "Eric Brown" <ecbrown@u.washington.edu>
Cc: <chemistry@ccl.net>
Subject: RE: Gaussian Molecular Integrals
Date: Mon, 25 Feb 2002 07:30:40 -0800
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I looked this book up on Amazon.

It costs $521.44

Who can afford that besides institutions?  That's way too much for even a
great science book.

Mark

=================================
Mark Thompson, Ph.D.
Planaria Software
Seattle, WA.
http://www.arguslab.com
=================================

> -----Original Message-----
> From: Computational Chemistry List [mailto:chemistry-request@ccl.net]On
> Behalf Of Andreas Goetz
> Sent: Monday, February 25, 2002 2:13 AM
> To: Eric Brown
> Cc: chemistry@ccl.net
> Subject: CCL:Gaussian Molecular Integrals
>
>
> Hi,
>
> the following book contains a good chapter about molecular integral
> evaluation:
>
>  Helgaker, Jorgensen, Olsen: Molecular Electronic-Structure Theory;
>  John Wiley & Sons, 2000.
>
>
> Greetings,
> 	Andreas
>
> On Sat, 23 Feb 2002, Eric Brown wrote:
>



From chemistry-request@server.ccl.net Mon Feb 25 11:54:31 2002
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Date: Mon, 25 Feb 2002 11:53:45 -0500
From: Aniko Simon <aniko@simbiosys.ca>
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Subject: Re: Cheminformatics
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Cheminformatics is Canada is growing strong.
There could be many starting points, but I would recommend the following:

Volume 15 of REVIEWS IN COMPUTATIONAL CHEMISTRY
Contains a comprehensive overview of the Canadian Computational Chemistry (up to 1999):
Russell J. Boyd, The Development of Computational Chemistry in Canada, pp. 213-299.

More information about the books can be found at
http://chem.iupui.edu/rcc/rccontents.html#vol15
(Volume 15, ISBN 0-471-36168-2)

In addition, there are a few new academic web sites:
http://www.cheminformatics.ca/
http://nmr.oci.utoronto.ca/gradopp.html
http://phm.utoronto.ca/~mdit/
http://biocomp.chem.unb.ca:8080/GD/
http://www.chem.yorku.ca/grad/

This list is far from exhaustive.

Hope this helps.
Regards,
Aniko

--
Aniko Simon Ph.D.
SimBioSys Inc., Toronto, Canada
t: (416) 741 4263
e: aniko@simbiosys.ca
w: http://www.simbiosys.ca/



leiyan wrote:

> I am interested in the Cheminformatics program and would like to get a Master degree in this field. Does anyone know if there are some programs in Canada?
>
> Many Thanks,
>
> Yan Lei
> Chemistry Library
> Zhongshan University
> Guangzhou, 510275
> P.R.China
>


