From chemistry-request@server.ccl.net Wed Apr 25 13:40:23 2001
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From: "Shobe, Dave" <dshobe@sud-chemieinc.com>
Subject: RE: CCL:G98W--no map to state 9
To: "'Stefan Grimme'" <grimmes@goofy1.uni-muenster.de>,
   "'CCL'" <chemistry@ccl.net>
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One thing that the input line doesn't make clear: hidden behind "chkbas" is
an ECP.  I'm actually using LANL2DZ with diffuse and polarization functions
added.  Anyway the pseudopotential is not inverse-square, so I don't know
what V/T should be.  

--David Shobe 

-----Original Message-----
From: Stefan Grimme [mailto:grimmes@goofy1.uni-muenster.de]
Sent: Wednesday, April 25, 2001 12:29 PM
To: Shobe, Dave
Subject: Re: CCL:G98W--no map to state 9


I saw that your V/T is quite off (2.6).
may be, your HF wavefunction is so bad
that the couplings in the CIS hamiltonian are
very large and the Gaussian Davidson solver
(which is very inefficient!) fails.
stefan
_________________________________________________________
Prof. Dr. Stefan Grimme
Organisch-Chemisches Institut (Abt. Theoretische Chemie)
Westfaelische Wilhelms-Universitaet, Corrensstrasse 40
D-48149 Muenster, Tel (+49)-251-83 36512/33241/36515(Fax)
Email:grimmes@uni-muenster.de
http://www.uni-muenster.de/Chemie/OC/research/grimme/
_________________________________________________________
Positions available for carrying out doctoral or
postdoctoral studies in chemistry in Münster:
http://www.uni-muenster.de/Chemie/OC/positions/
_________________________________________________________


From chemistry-request@server.ccl.net Wed Apr 25 19:45:56 2001
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Date: Wed, 25 Apr 2001 19:45:46 -0400
From: Doree F Sitkoff <doree.sitkoff@bms.com>
Subject: summary of dendrogram software
To: chemistry@ccl.net, Doree F Sitkoff <doree.sitkoff@bms.com>
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All -

Thanks for your input and sorry for the delay in posting the
summary.

-Doree

Original question:
Does anyone know of software (PC or UNIX-based) that can take a
distance matrix as input, perform clustering and display back
results as a dendrogram - of high enough quality that it could be
used for poster or publication purposes?

I have investigated SAS/JMP however it appears that it cannot
take a distance matrix as input - it must calculate the matrix
within the program.

MINITAB does appear to be able to do this, however I am wondering
what other options we might have.

Thanks,
-Doree

> From Egon Willighagen (egonw@sci.kun.nl):
Have a look at R, an OpenSource version of S, a statistical
program. I use it to do just the thing you're asking for... You
can download the software from www.r-project.org and use the
hclust function.

> From Gerd Raether (gerd@anterio.com)
Xcluster can do a Mosaic and Map display in postscript format and
write out customized cluster-data. Information you will find at
http://www.schrodinger.com/MacroModel/completdes.html#xcluster
For more information please contact schrodinger@anterio.com
(Europe) or help@schrodinger.com.
    (Note from Doree: The display is not so "pretty"...)

> From Peter Shenkin (shenkin@schrodinger.com):
Yes -- XCluster, (part of MacroModel). We print out something we
call the "clustering map" which contains the same info as the
dendrogram, but in a different format. (In geometric terms, I
believe it's the "dual".)  The "Dfile" method of XCluster takes
the distance matrix from a file, rather than computing it from an
ensemble of conformations. In this way, it can be used on
arbitrary preprocessed data.

> From Susan Atlas (susie@tangelo.phys.unm.edu):
We have used Matlab to do this but I would be interested in
hearing about any other options you find out about.

In addition, during informal discussions several people have
suggested investigating gene expression array software.




From chemistry-request@server.ccl.net Thu Apr 26 02:43:13 2001
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From: =?ks_c_5601-1987?B?wMzB+Mf1?= <mack@statchem.snu.ac.kr>
To: "ccl ccl" <chemistry@ccl.net>
Subject: Oniom Method in G98
Date: Thu, 26 Apr 2001 15:41:13 +0900
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Hello CCLers,

I would like to calculate the energy of Alanine dipeptide 
by using Oniom method in G98. But I had a error.
My input file is as follows.

# ONIOM(b3lyp/6-31g:/rHF/3-21g:rhf/sto-3g) Opt Test scf=direct opt=addredundant

aladi0_0

0 1
  C
  H    1 r2
  H    1 r3    2 a3
  H    1 r4    2 a4    3 d4
  C    1 r5    2 a5    3 d5 0 Me H
  O    5 r6    1 a6    2 d6 0 Me
  N    5 r7    1 a7    2 d7 0 Lo H
  H    7 r8    5 a8    1 d8 0 Lo
  C    7 r9    5 a9    1 d9 0 Lo
  H    9 r10    7 a10    5 d10 0 Lo
  C    9 r11    7 a11    5 d11 0 Lo
.
.
.

The error message of output is 

 ONIOM: saving gridpoint 1
 ONIOM: restoring gridpoint 6
 ONIOM: calculating energy.
 E23456=    -39.975185597776   -150.938892654677    -40.509698000197
           -152.051306592457   -486.521626565230
 EInt=      -.861910533745
 ONIOM: extrapolated energy =    -488.168552905431
 Recover reactant geometry.  Energy =  -.48816855D+03

 Symbolic Z-matrix:
 End of file in GetChg.
 Error termination via Lnk1e in /usr/local/g98/l101.exe.

What meaning is "End of file in GetChg"? or Do i have a error of
input file using Oniom method? Somebody help me!!!

Thx in advance.

============================================================
Jinhyuk Lee                 Email: mack@statchem.snu.ac.kr
School of Chemistry    Tel:   82-2-879-2721
Seoul National University
Seoul, Korea
============================================================


From chemistry-request@server.ccl.net Thu Apr 26 07:57:22 2001
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Date: Thu, 26 Apr 2001 13:56:53 +0200 (MET DST)
From: Ricardo Vivas-Reyes <rvivasre@vub.ac.be>
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Dear CCLers,


I would like to perform partial geometry optimizations in Gaussian, using
only cartesian coordinates? Is it possible

Thank you for your help. 

Ricardo. 

Ricardo Vivas-Reyes 
Dients Algemene Chemie 
Vrije Universiteit Brussel
Pleinlaan 2 1050 Brussels
Belgium 
Voice: 32 2/6293315 FAX:  32 2/6293317
E-Mail Address: rvivasre@vub.ac.be
______________________________________________



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From chemistry-request@server.ccl.net Thu Apr 26 08:49:38 2001
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    Dear Ricardo,
    I think that is not possible to perform partial geometry
optimization in gaussian using onle cartesian coordinates. The partial
optimization only works if the coordinate(s) to be frozen is an internal
coordinate.
        Best wishes,
                                    Silmar


From chemistry-request@server.ccl.net Thu Apr 26 10:51:42 2001
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From: "O.Nicolotti" <O.Nicolotti@sheffield.ac.uk>
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Hy,
does anybody know if there are somewhere some C programming 
routines for converting expressions from prefix to infix notations.

thanks,
Orazio

From chemistry-request@server.ccl.net Thu Apr 26 09:48:12 2001
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Dear all:
I have problems when trying to make the bond order analysis of a certain 
system, previously geomity-optimized, in gaussian98. The input file is 
as it follows:
%chk=wrod5_b
%mem=500Mb
#p rhf/6-31+g** Density=current SP AIM=BO

and the coputation stops with the following error message:

II-1. RING POINTS

-------------------------------------------------------------------------------
Ring                     Cartesian Coordinates          Attractors
                        X          Y          Z
-------------------------------------------------------------------------------
  1 ( 6-membered)    2.443335   0.559118  -0.700689       3   4  24  23  
25   5
REPAIRING RING  2: CASE 1, GAP OF LENGTH  1 BETWEEN ATTRACTORS 19  5

Irreparable ring damage: the gap cannot be bridged
Error termination via Lnk1e in /usr/local/modelling/g98/l609.exe.
Job cpu time:  0 days  0 hours 30 minutes  2.9 seconds.
File lengths (MBytes):  RWF=   50 Int=    0 D2E=    0 Chk=    2 Scr=    1

Is it necessary to calculate ring points or can it be avoided somehow? 
if not, how can I succesfully calculate the bond oreder in this system? 
I tryed directly with AIM, but found no option for this.
Can anyone tell me something???????????
Thanks in advance

-- 
Hugo G. de Teran Castañon
G. R. Informatica Biomedica
Institut Municipal de Investigacio Medica - IMIM
C/ Dr Aiguader, 80,E-08003/ Barcelona (SPAIN)
e-mail: hteran@imim.es
Ph: +34 93 221 10 09 ext 2340
Fax: Fax: +34 93 221 3237
		    
		    http://www1.imim.es/modeling



From chemistry-request@server.ccl.net Thu Apr 26 10:59:50 2001
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From: "Shobe, Dave" <dshobe@sud-chemieinc.com>
Subject: RE: Partial optimization in cartesian coordinates
To: "'CCL'" <chemistry@ccl.net>
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 <157A51F55AAAD3119CD70008C7B1629DDAAE58@lvlxch01.unitedcatalysts.com>
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I've not tried this, but apparently (from the manual) if you use
opt=modredundant, you can put an input line such as:

X 9 F

and this will freeze the cartesian coordinates of atom 9.  I do not know how
the input orientation to standard orientation conversion treats this!!

--David Shobe
Süd-Chemie Inc.
phone (502) 634-7409
fax     (502) 634-7724
email  dshobe@sud-chemieinc.com




From chemistry-request@server.ccl.net Thu Apr 26 12:04:20 2001
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Dear CCLers,

I am interested in the NMR coupling constant calculation for organic and
organometallic compounds.  I request your help for,
(a) Which method is more suitable for the calculation?
(b) What are the available programs?
(c) Is there some freely available programs for this?

Thanks in advance,

Giju T. Kalathingal

Department of Chemistry and Biochemistry
University of Delaware
Newark, Delaware 19716, USA.
E-mail: giju@udel.edu
URL: http://dogstar.duch.udel.edu/gijukt/welcome.html
Tel. ++1-302-831-2919
Fax: ++1-302-831-6335




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<!doctype html public "-//w3c//dtd html 4.0 transitional//en">
<html>

<blockquote TYPE=CITE>Hi,</blockquote>
It is possible to do it, and as matter of fact I did that before. (I can't
recall which version, g98 or g94, I used to do so). As I remember, if you
set opt=z-matrix and put your z-matrix as following form, then it will
do partial optimization:
<p>H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
x1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; y1&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; z1
<br>C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
x2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; y2&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; z2
<br>C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
x3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; y3&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; z3
<br>C&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
x4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; y4&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; z4
<br>H&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; 0&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
x5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; y5&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; z5
<p>x3&nbsp; 0.726704
<br>y3&nbsp; 0.000000
<br>z3&nbsp; 0.558749
<br>x4&nbsp; -0.726704
<br>y4&nbsp; 0.000000
<br>z4&nbsp; 0.558749
<br>x5&nbsp; 0.000000
<br>y5&nbsp; 0.000000
<br>z5&nbsp; 2.255480
<br>Constants
<br>x1&nbsp; 0.000000
<br>y1&nbsp; 0.000000
<br>z1&nbsp; -2.439287
<br>x2&nbsp; 0.000000
<br>y2&nbsp; 0.000000
<br>z2&nbsp; -0.688618
<p>In the above example, atom 1 and 2 are fixed, x, y, z are cartesian
coordinates.
<p>Frank
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;
<br>&nbsp;
<blockquote TYPE=CITE>&nbsp;&nbsp;&nbsp; Dear Ricardo,
<br>&nbsp;&nbsp;&nbsp; I think that is not possible to perform partial
geometry
<br>optimization in gaussian using onle cartesian coordinates. The partial
<br>optimization only works if the coordinate(s) to be frozen is an internal
<br>coordinate.
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Best wishes,
<br>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;
Silmar
<p>-= This is automatically added to each message by mailing script =-
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-- To Admins
<br>MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
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| Jan: jkl@ccl.net</blockquote>

<pre>--&nbsp;
&nbsp;Xiaofeng Frank Duan, Ph.D&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp; Phone: 937-904-8307
&nbsp;ASC MSRC&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; |&nbsp; Email: duanx@asc.hpc.mil&nbsp;&nbsp;&nbsp;
&nbsp;2435 5th St., ASC/HP Bldg. 676&nbsp;&nbsp;&nbsp; |&nbsp; URL:&nbsp;&nbsp; <A HREF="http://www.asc.hpc.mil">http://www.asc.hpc.mil</A>
&nbsp;Wright-Patterson AFB, OH 45433&nbsp;&nbsp;&nbsp; |</pre>
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From chemistry-request@server.ccl.net Thu Apr 26 14:46:56 2001
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From: Thomas E Sorensen <tes@csd.uwm.edu>
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Subject: CCL:Large file and Linux
To: chemistry@ccl.net
Date: Thu, 26 Apr 2001 13:46:55 -0500 (CDT)
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CCL members;

I want to run QM applications under Linux that use large files. 
I verified that the new Linux 2.4 Kernel supplied with RedHat 
7.1 (i386 version) supports files larger than 2 GIG. However, 
simple test programs compiled with gcc and g77 (version 2.96) 
terminate with "file size exceeded" errors when attempting to 
write a file larger than 2 GIG. 

Does anyone know if 64 bit ("long long") versions of header 
files and libraries exist that eliminate the 2 GIG file limit 
for Intel machines? If so, where do they reside?

Please send your responses directly to me at tes@uwm.edu. I will 
post a summary to the group if sufficient interest exists. 

Thank you in advance for your help.

Thomas Sorensen ( tes@uwm.edu )

From chemistry-request@server.ccl.net Thu Apr 26 17:09:58 2001
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From: "E.L. Willighagen" <egonw@sci.kun.nl>
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To: CHEMISTRY@ccl.net
Subject: LaTeX macro's for 14 Bravais Lattices?


Does anyone know about latex macro's to draw the 14 Bravais Lattices?

kind regards,

Egon Willighagen

