From chemistry-request@ccl.net Mon Sep 15 21:43:21 2003
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From: "Agrafiotis, Dimitris" <Dimitris.Agrafiotis$at$3dp.com>
To: "'chemistry$at$ccl.net'" <chemistry$at$ccl.net>
Subject: Quantifying the 'extendedness' of a molecular conformation
Date: Mon, 15 Sep 2003 21:42:48 -0400
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Dear CCL,

Is there a well-established measure of the 'extendedness' of a molecular
conformation? I am looking
for a single numerical value that can be used to compare conformations of
the *same* molecule (the
higher or lower the value, the more extended the conformation). Many things
come to mind, but I
was wondering if there is a measure that is well established in the
literature (the original references
would be of great help). Thanks in advance.

__________________________________________________
Dimitris K. Agrafiotis, Ph.D.
Johnson & Johnson Pharmaceutical Research & Development
665 Stockton Drive
Exton, PA 19341
USA
Tel: (610) 458-6045
Fax: (610) 458-8249
E-mail: dagrafio$at$prdus.jnj.com
http://www.dimitris-agrafiotis.com




From chemistry-request@ccl.net Mon Sep 15 23:18:30 2003
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From: "Somsak Tonmunphean" <somsak.t$at$chula.ac.th>
To: <CHEMISTRY$at$ccl.net>
Cc: "sirirat" <sirirat$at$atc.atccu.chula.ac.th>,
   "Vudhichai Parasuk" <parasuk$at$atc.atccu.chula.ac.th>,
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Subject: CCL:Only yellow contour maps in CoMFA
Date: Tue, 16 Sep 2003 10:17:47 +0700
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This is a multi-part message in MIME format.

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Dear CCL Members,

My M.Sc. student is doing CoMFA studies of antimalarial 1,2,4-trioxane =
compounds. She has some problems with her models. All the obtained =
models show steric contour maps with only yellow color, no green color. =
At the first time we thought she may make a mistake in setting up during =
the calculations. But when she carefully tried again with all the =
default settings, we got the same results. Therefore, we could not =
interpret these results. We do not know whether it can really be =
happened. If so, what does this mean?

Thank you,
Somsak Tonmunphean, Ph.D.
Department of Chemistry, Faculty of Science,
Chulalongkorn University, Bangkok 10330 Thailand            =20

------=_NextPart_000_0091_01C37C3B.C6C352B0
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</HEAD>
<BODY bgColor=3D#ffffff>
<DIV><FONT face=3DArial>Dear CCL Members,</FONT></DIV>
<DIV><FONT face=3DArial></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial>My M.Sc. student is doing CoMFA studies of =
antimalarial=20
1,2,4-trioxane compounds. She&nbsp;has some problems with her models. =
All the=20
obtained models&nbsp;show steric contour maps with only =
yellow&nbsp;color, no=20
green color. At the first time we thought she may make a mistake in =
setting=20
up&nbsp;during the&nbsp;calculations. But when she carefully&nbsp;tried =
again=20
with all the default settings, we got the same results. Therefore, we =
could not=20
interpret these&nbsp;results. We do not know whether it can&nbsp;really =
be=20
happened. If so, what does this mean?</FONT></DIV>
<DIV><FONT face=3DArial></FONT>&nbsp;</DIV>
<DIV><FONT face=3DArial>Thank you,</FONT></DIV>
<DIV><FONT face=3DArial>Somsak Tonmunphean, Ph.D.<BR>Department of =
Chemistry,=20
Faculty of Science,<BR>Chulalongkorn University, Bangkok 10330=20
Thailand&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp=
;&nbsp;&nbsp;</FONT></DIV></BODY></HTML>

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From chemistry-request@ccl.net Tue Sep 16 02:32:20 2003
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Date: Tue, 16 Sep 2003 11:37:41 +0530 (IST)
From: Gyanendra kumar <gyan)at(mbu.iisc.ernet.in>
To: Katie Doucet <kgdct)at(mta.ca>
cc: chemistry)at(ccl.net
Subject: Re: CCL:free docking program
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Hi Katie,
Autodock is one such program. Another one is Dock. Give a search in 
google.com and you will find the homepages of these freewares.

Gyan.

On Mon, 15 Sep 2003, Katie Doucet wrote:

> To whom it may concern;
> 
> I was wondering if there was any freeware or at least free to academic 
> institutions with the capability of DOCKING a substrate molecule inside an 
> enzyme active site. If you know of any such a program could you please let me 
> know.
> 
> Thanks
> 
> -k.Doucet 
> Mount Allison University
> 
> 
> -= This is automatically added to each message by the mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
> and send your message to:  CHEMISTRY)at(ccl.net
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> 
> 
> 
> 
> 
> 

-- 
********************************************
Gyanendra Kumar (Research Student),
Prof. A. Surolia's Lab,
#204, Molecular Biophysics Unit,
Indian Institute Of Science,
Bangalore, PIN-560012.INDIA,
Phone 91-80-293-2389,-2714(Lab), -2539(Res).
http://mbu.iisc.ernet.in/~surolia/gyan.html
********************************************
Residence: R-17, Students Hostel, IISc.
********************************************


From chemistry-request@ccl.net Tue Sep 16 08:17:12 2003
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Date: Tue, 16 Sep 2003 14:16:35 +0200
To: chemistry[at]ccl.net
Subject: Thymine dipole-moment
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Hi,

I need to compare a calculated dipole moment of thymine in the gas phase
with the experimental value. The only source I've found so far is: I.
Kulakowska et al, Biochim. Biophys. Acta 361 (1971) 119-130 "Dipole
moments of 2,4-diketopyrimidines Part II: Uracil, Thymine and their
derivatives. They give dipole moment of 4.13 D. but it was mesured in
dioxane.

Is anybody aware of another source for thymine dipol moment in the gas
phase???

Thanks in advance
  Dan

-- 
Daniel Svozil, PhD
Institute of Organic Chemistry and Biochemistry
and Center for Complex Molecular Systems and Biomolecules
http://www.molecular.cz/
Czech Republic

phone: +420-2-20 183 263


From chemistry-request@ccl.net Tue Sep 16 03:26:14 2003
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Date: Tue, 16 Sep 2003 09:26:33 +0200
From: Felipe Pineda <pineda[at]imb-jena.de>
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Subject: Re: CCL:Autodock and Rigid Body Docking
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hi Chris,

a little bit late, but better than never ;-)

take a look at the following paper by my former boss, Martin Zacharias:

Zacharias, M.Protein-protein docking with a reduced protein model accounting for
side-chainflexibility.Protein Sci  12(2003)1271-82

Maybe you can then contact him directly for more details.

Best regards

Felipe

Dominique Vlieghe schrieb:

> Hi Chris,
>
> In AutoDock, the ligand is made flexible by defining the torsion angles
> that should vary. If you chose 0 torsion angles, your ligand would be
> regarded as being rigid. Furthermore, you can chose whichever torsion
> angle you desire to be kept flexible, as long as you do not have more
> than 32. This means about 8-16 side chains, depending on their size. Of
> course, the target will always be rigid...
>
> Someone else replied to you that ZDock is a good tool to do
> protein-protein docking. I agree with him when the two proteins have
> conformation very similar to the bound conformations. The perfomance
> however drops considerably when you work with homology models. I must
> say that I did not test RDock yet.
>
> (...)

--
Dr. Luis Felipe Pineda De Castro
EnTec GmbH
Structural Bioinformatics and Drug Design
Adolf-Reichwein-Str. 20        Phone:  3641-65-8445
D-07745 Jena,                  Fax:    3641-65-8436
GERMANY
e-Mail: pineda[at]imb-jena.de
web   : http://www.entec-jena.de




From chemistry-request@ccl.net Tue Sep 16 03:45:25 2003
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To: Katie Doucet <kgdct[at]mta.ca>
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Subject: Re: CCL:free docking program
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hi katie,

just have a look at:

http://www.scripps.edu/pub/olson-web/people/gmm/

Katie Doucet wrote:

> To whom it may concern;
> 
> I was wondering if there was any freeware or at least free to academic 
> institutions with the capability of DOCKING a substrate molecule inside an 
> enzyme active site. If you know of any such a program could you please let me 
> know.
> 
> Thanks
> 
> -k.Doucet 
> Mount Allison University
> 
> 
> -= This is automatically added to each message by the mailing script =-
> To send e-mail to subscribers of CCL put the string CCL: on your Subject: line
> and send your message to:  CHEMISTRY[at]ccl.net
> 
> Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST[at]ccl.net 
> HOME Page: http://www.ccl.net   | Jobs Page: http://www.ccl.net/jobs 
> 
> If your mail is bouncing from CCL.NET domain send it to the maintainer:
> Jan Labanowski,  jkl[at]ccl.net (read about it on CCL Home Page)
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> 
> 
> 
> 
> 
> 
> 


-- 
********************************************************
    BIOT Christophe
    Inginierie Biomoliculaire, CP 165/64
    Universiti Libre de Bruxelles
    50 Av. F.D. Roosevelt
    1050 Bruxelles, BELGIQUE

Phone: 32-2-650 3001
Fax:   32-2-650 3606
E-mail:cbiot[at]ulb.ac.be
********************************************************

                ::>>>OUT NOW <<<<::
	
Basis Set and Electron Correlation Effects
on ab Initio Calculations of Cation-pi/H-Bond Stair Motifs
Wintjens, R.; Biot, C.; Rooman, M.; Lievin, J.
J. Phys. Chem. A.; 2003; 107(32); 6249-6258.





From chemistry-request@ccl.net Tue Sep 16 09:25:02 2003
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Date: Tue, 16 Sep 2003 15:24:29 +0200 (MEST)
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To: chemistry~at~ccl.net
Subject: CCL:Re: Quantifying the 'extendedness' of a molecular conformation
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To: <chemistry~at~ccl.net>
Subject: CCL:Re: Quantifying the 'extendedness' of a molecular conformation

There are many measures of the extendedness. I assume for clarity that
the molecule is modelized by a set of points. There are:
- The generalized diameter, i.e. the highest straight distance between
two points of the set
- The generalized radius, i.e. the highest straight distance from
the center, or simpler, the radius of the smallest sphere enclosing
the set. /* care: the radius is not, in general, half of the diameter */
- Various shape coefficients, based on surface or volume of the convex
hull of the set (the convex hull is the smallest polyhedron enclosing
the set).

All these quantities are computed by the RADI freeware, to be
downloaded (with documentation containing references), from:

http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#RADI

Michel Petitjean,                     Email: petitjean~at~itodys.jussieu.fr
ITODYS (CNRS, UMR 7086)                      ptitjean~at~ccr.jussieu.fr
1 rue Guy de la Brosse                Phone: +33 (0)1 44 27 48 57
75005 Paris, France.                  FAX  : +33 (0)1 44 27 68 14
http://petitjeanmichel.free.fr/itoweb.petitjean.html

>From: "Agrafiotis, Dimitris" <Dimitris.Agrafiotis~at~3dp.com>
>Dear CCL,
>
>Is there a well-established measure of the 'extendedness' of a molecular
>conformation? I am looking
>for a single numerical value that can be used to compare conformations of
>the *same* molecule (the
>higher or lower the value, the more extended the conformation). Many things
>come to mind, but I
>was wondering if there is a measure that is well established in the
>literature (the original references
>would be of great help). Thanks in advance.
> 
>__________________________________________________
>Dimitris K. Agrafiotis, Ph.D.
>Johnson & Johnson Pharmaceutical Research & Development
>665 Stockton Drive
>Exton, PA 19341
>USA
>Tel: (610) 458-6045
>Fax: (610) 458-8249
>E-mail: dagrafio~at~prdus.jnj.com
>http://www.dimitris-agrafiotis.com


From chemistry-request@ccl.net Tue Sep 16 19:01:01 2003
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Date: Tue, 16 Sep 2003 19:05:41 -0400
To: chemistry{at}ccl.net
From: Joe Leonard <jle{at}theworld.com>
Subject: CD's mac/pc
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Folks, has anybody burned CD-R or CD-RW's on Mac's
and read them on Linux/PC's?  Is this a straightforward
process, or is it like the old days where each machine's
formats are inaccessible to each others?

Sorry for the naive question, but there's no Apple store withing
an hour or so, and I figure SOMEBODY's tried this out there...

Thanks in advance!

Joe



From chemistry-request@ccl.net Tue Sep 16 09:52:50 2003
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Date: Tue, 16 Sep 2003 09:51:20 -0400 (EDT)
From: Zhi-Xiang Wang <zxwang{at}sunchem.chem.uga.edu>
To: chemistry{at}ccl.net
Subject: Control convergene threshold in Gaussian
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Hi
  Do we have a method to make the convergene threshold in Gaussian like 
that

                               Threshold   
 Maximum Force                  .000050     
 RMS     Force                  .000300     
 Maximum Displacement           .018800    
 RMS     Displacement           .012000     

Instead of the default values 

         Item                Threshold  
 Maximum Force               .000450     
 RMS     Force               .000300     
 Maximum Displacement        .001800     
 RMS     Displacement        .001200    

Thanks

Zhixiang




From chemistry-request@ccl.net Tue Sep 16 19:01:55 2003
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From: Elmar Gerwalin <elg_at_chemie.uni-kl.de>
Reply-To: elg_at_chemie.uni-kl.de
To: chemistry_at_ccl.net
Subject: SCRF - visualization of tesserae in G98
Date: Wed, 17 Sep 2003 01:01:20 +0200
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Hello !

I'd like to know if and how it's possible to get more information about the  
surface tesserae that are generated by a SCRF calculation using G98.

Finally, I'd like to visualize them, but a table of their coordinates (are 
they always triangular ?) or something like that would help, too.

Any help is appreciated.

Bye
Elmar

-- 
========================================================
Elmar Gerwalin ,   University of Kaiserslautern,Germany
                            Dept. of Theoretical Chemistry
                            elg_at_chemie.uni-kl.de    
========================================================




From chemistry-request@ccl.net Tue Sep 16 23:06:25 2003 -0400
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Date: Tue, 16 Sep 2003 20:06:23 -0700 (PDT)
From: Juraina Jamil <jaj_75{at}yahoo.com>
Subject: Assignment of root, branch, etc., in autotors in autodoc
To: chemistry{at}ccl.net

Hello everyone, 

I am a little bit confused as to the assignment of
root, branch etc in autotors in autodock in regards
to peptide docking.  I tried choosing the various roots
prompted by the autotors program and after docking,
it seems that my peptide is in pieces.  And so I tried
defining the root at the center of the molecule
using the -r flag but I still get back the same thing. 
Can anyone give me a tip or two as to how I should go
about this? 

-Juraina-

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