From chemistry-request@server.ccl.net Tue Sep  4 00:02:21 2001
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Date: Fri, 4 Jan 2002 12:2:8 +0800
From: Song Yun-long <songyunlong@263.net>
To: "chemistry@ccl.net" <chemistry@ccl.net>
Subject: Scoring functions in database searching
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Dear sir,
I am very interested in scoring functions used in database searching,as consensus 
score gives the best result.I know there are many scoring functions,such as PMF,
PLP(Piecewise Linear Potential),Chemscore,FlexX and Gold and Score which was developed
by Lai et.al.

I want to know if the scoring functions described above are free.Is there any other scoring 
functions?

Best wihes to you!
                              
Yours sincerely,

Song Yun-long,Ph.D

~~~~~~~~~~~~~~~~~~~~~~~~~~
Dept of med.chem
School of pharmacy
Second Mil Med Univ
Guohe Road,325
Shanghai,200433
P.R.China
E-mail:songyunlong@263.net
Tel:86-21-25070248
~~~~~~~~~~~~~~~~~~~~~~~~~~
            


From chemistry-request@server.ccl.net Tue Sep  4 07:14:16 2001
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Date: Tue, 04 Sep 2001 13:17:43 +0200
From: Oliver Hucke <hucke@uni-freiburg.de>
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Dear CCLer's,

we want to fit a modelled protein structure into an existing 3D electron
density map obtained by electron microscopy.
The map was produced by the program imagic (file format .img/.hed) and
we would like to use VMD for the visualization of the protein structure
and the electron density surface. Unfortunately VMD can not handle the
.img-format.

Does somebody know how to convert the .img into an VMD-readable file?
Any program suggestions for the docking procedure?

Kind regards,

Oliver.
--
______________________________________

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

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



From chemistry-request@server.ccl.net Tue Sep  4 07:43:54 2001
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Hi every one,
I am interested by comparing linear free energie relation-chips
experimental and theoretical results.
These experimental results are based on single and multiple amino-acids
mutations.
I'd like to know if anyone knows a free software to do these mutation in
silico.

Thank's in advance.

Mignon Pierre
PhD student
Free University of Brussels (VUB)


From chemistry-request@server.ccl.net Tue Sep  4 10:05:29 2001
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I am attempting to do some NBO analysis of systems
using Gaussian98. They are essentially a +3 lanthanide
centre and a neutral tridentate nitrogen-bearing ligand,
giving the system an overall charge of, obviously, +3.

The input file is set to do a geometry optimisation,
but this is never reached as the calculation fails 
after the first SCF cycle with:
</snip/>
       /RESON  / : Allow strongly delocalized NBO set

 Analyzing the SCF density

 Job title: Gaussian generated by
Cerius2                                   

 Storage needed:    283944 in NPA,    376394 in NBO (   6291456
available)

 Subroutine NAOANL could not find a f-type valence orbital on atom La 1.
 IVAL :  1  0  0  1     M :  1     LA :  1
 Error
 Error termination via Lnk1e in /home/chem/scsprida/g98/l607.exe.
</snip/>

I am using the Stuttgart ECP's for the lanthanide centre (in this case
it's Lanthanum) and 6-31(g) for the remainder of the atoms.

Any ideas?
Does this suggest (as I fear it does) that NBO analysis with lanthanides
(more specifically f-orbitals) is either not possible or very awkward?

Regards,

-- 
Tris Youngs - e-mail: T.G.A.Youngs@reading.ac.uk
+Department of Chemistry, University of Reading
+Whiteknights Campus, Reading, RG6 6AD, England
"I don't know what's more annoying - my failure
to formulate a unified theory..... or you".
-Stephen Hawking to Homer

From chemistry-request@server.ccl.net Tue Sep  4 12:13:46 2001
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Date: Tue, 4 Sep 2001 12:14:51 -0400
From: Wei Zhuang <weiz@mail.rochester.edu>
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To: chemistry@ccl.net
Subject: the minimum distence between solute molecule and chloroform
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Hi,all:

I am doing a simulation of an organic molecule in the solvent of
chloroform,please tell me where can I find the minimum distence of solute
and solvent(chloroform).

regards

wei zhuang
weiz@mail.rochester.edu


From chemistry-request@server.ccl.net Tue Sep  4 12:57:35 2001
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Date: Tue, 4 Sep 2001 20:03:54 +0300
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Dear CHEMISTRY,

I am wondering if Se was parameterized for INDO/1s (ZINDO/S) method.
Also, I would like to ask for your advice on best basis set for Se for
ab initio calculations. I need compare results for O-S-Se compounds

Best regards,
 Mike                          mailto:MikePeleah@yahoo.com



From chemistry-request@server.ccl.net Tue Sep  4 10:23:42 2001
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"Graeme L. Nyberg" wrote:

> As previously posted on 29 June 01:
>
> "There is a tremendous, free, program called MacMolPlt (for the Mac)
> which operates both as a front- and rear-end to Gamess (US at least).
> It prepares the input file, and shows the 3D structure of the
> molecule. It reads the output files, and can display MOs, vibrations,
> etc. Combined with the Mac version of Gamess this makes a great
> package (especially for teaching)."
>
> Unfortunately there is no PC version of MacMolPlt. It is sufficiently
> good, though, that you might consider switching to Macs!
>
> Graeme Nyberg.

But what if someone (in this case a college) has spent thousands of dollars on
pc's,
do they just throw them away because of ONE program?

Richard

--
Richard L. Wood, Ph. D.
Physical/Computational Chemist
Post-doctoral Associate
Department of Food Science
120 Stocking Hall
Cornell University, Ithaca, NY 14853





From chemistry-request@server.ccl.net Tue Sep  4 12:49:03 2001
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Dear CHEMISTRY,

I am looking for reviews dealing with Quantum Chemistry Applications
for Analytical Chemistry. Could anybody help me?

Best regards,
 Mike                          mailto:MikePeleah@yahoo.com



From chemistry-request@server.ccl.net Tue Sep  4 12:05:29 2001
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Date: 04 Sep 01 09:59:48 -0400
From: Kam Chana <ksc@camsoft.com>
Subject: RE: CCL:GUI for GAMESS
To: chemistry <chemistry@ccl.net>, "Ha-Yeon Cheong" <hcheong@bowdoin.edu>
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         Reply to:   RE: CCL:GUI for GAMESS
The current version of CambridgeSoft Chem3D (v6.0) provides a GUI for Gamess that is avaialble for the Windows platform.  Chem3D offers model building and visualization capabilities and a simple GUI for management of Gamess calculations.  We offer a compiled version of Gamess that will work with Chem3D through the official Gamess site (http://www.msg.ameslab.gov/GAMESS/GAMESS.html)  
Sincerely

Kam Chana
CambridgeSoft

Ha-Yeon Cheong wrote:
>Dear fellow CCL folks,
>
>We were interested in a freeware program that provides a GUI for >GAMESS/PCGAMESS. We are trying to use PC GAMESS for the computational >class in our college, and it would seem that a GUI interface would >facilitate the job of using PC GAMESS for the average student.
>
>Thank you for your attention and I eagerly await your response.
>
>Yours,
>Ha Yeon Cheong
>
>Ha Yeon Cheong
>Bowdoin College
>Chemistry Intern
>
>
>
>-= This is automatically added to each message by mailing script =-
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>
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From chemistry-request@server.ccl.net Tue Sep  4 14:04:18 2001
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Date: Tue, 4 Sep 2001 14:04:17 -0400 (EDT)
From: Jan Labanowski <jkl@ccl.net>
To: chemistry@ccl.net
cc: Jan Labanowski <jkl@ccl.net>
Subject: How to support CCL -- a short course with examples 
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Dear CCL Establishment... (You see how satisfying I am trying to be...)

Several people asked me for details on supporting CCL financially,
So I will share it with all of you (there may be some of you who
"always wanted to know, but were afraid to ask"). Please read on, and
have a change of heart.  I admit that on the CCL Web site I am caught in
the impossible catch 22 -- should I first make people happy about supporting
CCL, or should I tell them first how to support it. Anyhow... If you consider
this resource useful, help me keep it and grow it... 

How can you help CCL?

  1) By giving me a DONATION which is tax deductible at least in the US (we
     are an academic organization and you will get a thank-you-letter from
     The Ohio State University confirming your donation and you can use it
     for tax purposes). Just send (Jan Labanowski) a check made to:
           OSC Development Fund (CCL)
     You can also FAX (614-688-3998) me a simple form if you prefer to charge
     it to a Visa or MC:

                  OSC Development Fund (CCL)

         Amount of CCL Donation:.......................

         Your Name on the Credit Card:.................

         Credit Card (Visa or MC)......................

         Credit Card Number:...........................

         Expiration Date on the card: .................

         Signature and date: ..........................  

     Use the FAX number: 614-688-3998 which is located in the OSC business
     office and is under lock and key (i.e., your Credit Card Number is safe)..
     Do not hesitate to give me a donation, if you can give me only small
     amount (say, 30 USD is practically the smallest donation that my OSC
     accountants want to process). Many small donations will do too {:-)}.
     And beside, if I hava a large number of donationa, I can claim wide
     community support which may help me a bit in twisting some arms when
     I need to show the need for CCL and the good publicity it brings to my
     parent organization.

     If you (or your institution) gives me 500 USD or more, I will place
     your logo-and-link on any CCL page you desire (send me e-mail where
     you want it, or I will bug you anyhow for this information, once I get
     the money from you).
     
  2) You CAN BUY one (or more) CCL Archives Sets on CD. They contain copies
     of all files from the CCL Web and FTP site. They are 250 USD
     a piece. You can send me a check, or FAX a simple order to the FAX
     given above. You can also send me a Purchase Order, and Bank transfers
     and whatever. Send me e-mail, and I will provide you with quotations,
     and information, and whatever else your "pencil pushers" need to be
     happy and needed. This payment is not tax deductible, since it is
     a service/sale. Which charge not for the information on them, but the
     work needed to produce them. This is a set of 4 CDs (about 2 Gigabytes
     of files) which are burned always fresh.  You can mount them on your
     local machine, and browse/search/grep them locally rather then use a slow
     or busy network. You can easily justify it in your project, since there
     is a lot of information and software on these CDs. I will thank you on
     the Supporters Page (which is accessible from the CCL home page:
          http://www.ccl.net
     and if you buy more than 2 CD sets (i.e., 3 sets or more), I will thank
     you in a similar way, I am thanking the major donors (i.e., logo/link on
     the page of your choice). Talk to me... (and pay... {:-D} ).

  3) Of course, some people cannot help financially and they may need money
     even more then I do. But all of you can help with contributing new
     material to the archives, good discussions on the list, and with your
     comments and suggestions. If your contribution is good and thoughful,
     it may be worth a real gold for the CCL.

And so... (sorry, I could not resist the popular cliche...), my fellow CCL
subscribers: ask not what your CCL can do for you--ask what you can do
for your CCL. [Source: http://www.cs.umb.edu/jfklibrary/j012061.htm -- 
Gosh... was his speach writer good...].

There is more information about CCL on CCL web site:
    http://www.ccl.net/chemistry/aboutccl/supporting

As an example of my contribution to the CCL archives, check:
   http://www.ccl.net/cca/software/UNIX/netfilter/
a step by step instructions on how to use an old PC to create a powerful
firewall (protect your computers) and masquarading router (attach many
computers to a single IP address, and they will look like each has its
own IP address) for your home or office (BTW, comments and fixes welcome).

Jan

Jan K. Labanowski            |    phone: 614-292-9279,  FAX: 614-292-7168
Ohio Supercomputer Center    |    Internet: jkl@ccl.net 
1224 Kinnear Rd,             |    http://www.ccl.net/chemistry.html
Columbus, OH 43212-1163      |    http://www.ccl.net/



From chemistry-request@server.ccl.net Tue Sep  4 16:35:52 2001
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Date: Tue, 4 Sep 2029 16:46:45 -0500
From: wei zhuang <weiz@mail.rochester.edu>
To: "Shobe, Dave" <dshobe@sud-chemieinc.com>
CC: "chemistry@ccl.net" <chemistry@ccl.net>
Subject: Re: RE: the minimum distence between solute molecule and chloroform
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Hi, thank you for your reply.

I am doing classical MD simulation.


wei zhuang
weiz@mail.rochester.edu
>It might help if you told us what kind of simulation you were doing: ab
>initio dielectric continuum, classical molecular dynamics, etc.  
>
>--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: Wei Zhuang [mailto:weiz@mail.rochester.edu] 
>Sent: Tuesday, September 04, 2001 12:15 PM
>To: chemistry@ccl.net
>Subject: CCL:the minimum distence between solute molecule and chloroform
>
>
>Hi,all:
>
>I am doing a simulation of an organic molecule in the solvent of
>chloroform,please tell me where can I find the minimum distence of solute
>and solvent(chloroform).
>
>regards
>
>wei zhuang
>weiz@mail.rochester.edu
>
>
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                    ÖÂ
Àñ£¡

            wei zhuang
            weiz@mail.rochester.edu



From chemistry-request@server.ccl.net Tue Sep  4 18:41:29 2001
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Date: Wed, 5 Sep 2001 01:41:27 +0300 (EET DST)
From: John Kerkines <jkerkin@cc.uoa.gr>
To: chemistry@ccl.net
Subject: Hewlett Packard merges with Compaq 
Message-ID: <Pine.GSO.3.96.1010905013916.17560C-100000@nikias.cc.uoa.gr>
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Content-Type: TEXT/PLAIN; charset=US-ASCII

I think this is something very interesting to all of us. More information:

http://www.cnn.com/2001/TECH/industry/09/04/hp.compaq.consumer/index.html
http://www.hp.com/hpinfo/newsroom/press/04sep01a.htm
http://www.compaq.com/newsroom/pr/2001/pr2001090402.html

Regards,
Ioannis Kerkines


