From chemistry-request@server.ccl.net Tue Nov 5 06:27:18 2002 Received: from kintaro.grt.kyushu-u.ac.jp ([133.5.48.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA5BRHC04243 for ; Tue, 5 Nov 2002 06:27:18 -0500 Received: from kentaro.grt.kyushu-u.ac.jp ([3.4.1.213]) by kintaro.grt.kyushu-u.ac.jp (8.11.6+Sun/3.7W) with ESMTP id gA5BRG525693 for ; Tue, 5 Nov 2002 20:27:17 +0900 (JST) Received: from xenowin ([3.4.12.140]) by kentaro.grt.kyushu-u.ac.jp (8.10.2+Sun/3.7W) with SMTP id gA5BRGm25505 for ; Tue, 5 Nov 2002 20:27:16 +0900 (JST) From: Yoshihiro NISHIDA To: chemistry@ccl.net Date: Tue, 05 Nov 2002 20:25:54 +0900 X-Priority: 3 (Normal) Message-Id: Subject: AutoDock about constrain distance MIME-Version: 1.0 Content-Type: text/plain; charset="shift_jis" X-Mailer: Opera 6.05 build 1140 Dear AutoDock user I have been using AutoDock 3.0.5 to do enzyme-ligand docking simulations. I want to do distance constraint between atoms of enzyme and ligand to do docking simulation,because my ligand is too large to fit into the binding site. Could you tell me how to do that? Or give me any idea. thanks in an advance. --------------------------- genetic resorce technology Kyushu univercity YOSHIHIRO NISHIDA heineken@grt.kyushu-u.ac.jp --------------------------- From chemistry-request@server.ccl.net Tue Nov 5 07:17:44 2002 Received: from fermat.chemres.hu ([193.224.146.183]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id gA5CHhC05906 for ; Tue, 5 Nov 2002 07:17:43 -0500 Received: from stark.udg.es (IDENT:pedro@fermat.chemres.hu [127.0.0.1]) by fermat.chemres.hu (8.11.6/8.11.6) with ESMTP id gA5CHhw23298 for ; Tue, 5 Nov 2002 13:17:44 +0100 Sender: pedro@chemres.hu Message-ID: <3DC7B6E7.D860DD01@stark.udg.es> Date: Tue, 05 Nov 2002 13:17:43 +0100 From: Pedro Salvador X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.7smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Wigner's theorem Content-Type: multipart/alternative; boundary="------------8FFBBBDBD7F6FFFAF2C6F82D" --------------8FFBBBDBD7F6FFFAF2C6F82D Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers, I'm looking for demonstrations of Wigner theorem in Perturbation Theory, namely, how energy corrections up to orders 2n and 2n+1 can be _exactly_ obtained from n-th order eigenfunction corrections. Can some of you point me to proper references? I will summarize responses. Thanks in advance! Emili Besalu emili@iqc.udg.es Institute of Computational Chemistry University of Girona. Spain --------------8FFBBBDBD7F6FFFAF2C6F82D Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers,

I'm looking for demonstrations of Wigner theorem in Perturbation Theory,
namely, how energy corrections up to orders 2n and 2n+1 can be
_exactly_ obtained from n-th order eigenfunction corrections.
Can some of you point me to proper references?
I will summarize responses.

Thanks in advance!

Emili Besalu
emili@iqc.udg.es
Institute of Computational Chemistry
University of Girona. Spain 


 

--------------8FFBBBDBD7F6FFFAF2C6F82D--



From chemistry-request@server.ccl.net Tue Nov  5 05:01:45 2002
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From: Stewart Kirton 
To: "'chemistry@ccl.net'" 
Subject: MOPAC Output in Insight II
Date: Tue, 5 Nov 2002 10:00:18 -0000 
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Hi all,

I am attempting to calculate the electrophilic frontier values for a series
of aromatic compounds using the AMPAC/MOPAC module within Insight II -
essentially trying to reproduce the results obtained by Ackland (Xenobiotica
1993 23(10) 113501144). The problem is that I am unable to extract this data
> from the output that is generated via the Insight II interface as it is not
obvious to me where I should be looking, and was hoping that there may be
someone out there who could give me some pointers, as to where this data is
in the .out file.

Many thanks in advance for any assistance
Best Wishes
Stewart

> *********************************************
> Stewart Kirton
> Research Associate
> 
> Astex Technology Ltd
> 250 Cambridge Science Park
> Milton Road, Cambridge
> CB4 0WE, UK
> 
> Tel:  +44(0)1223 435030
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> s.kirton@astex-technology.com
> 
> www.astex-technology.com
> 
> *********************************************
> 


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From chemistry-request@server.ccl.net Tue Nov  5 10:04:52 2002
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From: VITORGE Pierre 094605 
To: "'ZHIJIAN WU'" , chemistry@ccl.net
Subject: RE: cpcm converge problem
Date: Tue, 5 Nov 2002 16:00:45 +0100 
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Did you ask Official Gauusain help, whether they know any bugg on their
scrf?

Pierre Vitorge


-----Message d'origine-----
De: ZHIJIAN WU [mailto:zjwu@chem1.chem.dal.ca]
Date: lundi 4 novembre 2002 14:22
À: chemistry@ccl.net
Objet: CCL:cpcm converge problem


Hi,

Thanks for the reply about my questions on the optimization of 
charged species in solution from Dr. John Mckelvey and Dr. 
Andreas Klamt. 
However, when I tried to optimize the charged molecules with PCM 
(DPCM) and CPCM (Cosmo), it seems the optimization nevers 
converges (oscillating). Before the PCM and CPCM calculation, the 
optimization of the same charged molecules converges very well on 
the gas phase and solution using Onsager model. Is there any 
comments on what keywords should I put in order to converge 
using PCM or CPCM models? During the 
CPCM optimization, I also got some warning message as follows:
>.......
#b3lyp/6-31g(d,p) opt=readfc scrf=cpcm
>.....
Warning: electronic charge 138 neglected
 Warning: electronic charge 148 neglected
 Warning: electronic charge 400 neglected
  Added Sphere     Between       RE            Surface
        17       15 and  4    1.28715          1.14982
        18       15 and 10    1.64526          2.70163
 ------------------------------------------------------
 
----------------------------------------------------------------------------
--
     AT CONVERGENCE
  469 Tesserae over a maximum of 1500
  Surface Area (Ang**2) =  240.17308
  Volume       (Ang**3) =  251.83557
 Error on NUCLEAR pol.charges = 0.02780 Error on ELECTR. 
pol.charges 
=-0.04214 

>...................
Warning: electronic charge 473 neglected
 Electronic charge 477 has a negative value:   -0.613816
 Hint: increase the number of tesserae or change the molecule 
orientation
 Warning: electronic charge 146 neglected
 Warning: electronic charge 151 neglected
 Warning: electronic charge 473 neglected
 Electronic charge 477 has a negative value:   -0.613816
 Hint: increase the number of tesserae or change the molecule 
orientation
  Added Sphere     Between       RE            Surface
        17       15 and 10    1.64067          3.21324
 ------------------------------------------------------
 
----------------------------------------------------------------------------
--
     AT CONVERGENCE
  477 Tesserae over a maximum of 1500
  Surface Area (Ang**2) =  240.46224
  Volume       (Ang**3) =  251.42256
 Error on NUCLEAR pol.charges = 0.01528 Error on ELECTR. 
pol.charges 
=-0.03025
 
----------------------------------------------------------------------------
--
Any comments?  Should I increase Tesserae points (I use the 
default, 60)? Many thanks.

Z. J. Wu
Department of Chemistry
Dalhousie University
Canada


>From: jmmckel@attglobal.net 
>Reply-To: jmmckel@attglobal.net 
>To: "Dr. Andreas Klamt" 
>CC: Zhijian Wu , chemistry@ccl.net 
>Subject: Re: CCL:solvation energy 
>Date: Fri, 27 Sep 2002 15:26:46 +0000 
> 
>In addition, a molecule with 0.0 dipole moment might not get 
solvated 
in a dipole model... charged or not, ... say 1,4 dioxane, or 
>1,4 diazine..certainly soluble in a lot of solvents... Also, one can 
disolve 
1gr of benzene per liter of water. 
> 
> 
>John McKelvey 
>"Dr. Andreas Klamt" wrote: 
> 
> > For a charged species the dipole moment is only defined if you 
specify an almost arbitrary reference point. Anyway, solvation 
> > energies for charged species mainly depend on the details of 
the 
charge distribution and they strongly depend on the shape of 
> > the cavity. Just forget about simple Onsager models. Use PCM 
or 
COSMO. 
> > 
> > Andreas Klamt 
> > 
> > Zhijian Wu schrieb: 
> > > 
> > > Hi, cclers, 
> > > 
> > > Does anyone know that for the charged speices (say, +1 and 
-1), 
how accurate of the Onsager Model (based on dipole moment) on 
> > > the solvation energy? 
> > > 
> > > Thank you very much for your help! 
> > > 
> > > Regards, 
> > > 
> > > Zhijian Wu 
>
> > Dr. Andreas Klamt 
> > COSMOlogic GmbH&CoKG 
> > Burscheider Str. 515 
> > 51381 Leverkusen, Germany 
> > 
> > Tel.: 49-2171-73168-1 Fax: ...-9 
> > e-mail: andreas.klamt@cosmologic.de 
> > web: www.cosmologic.de 
> > ---------------------------------------------------------------------
----------- 
> > COSMOlogic 
> > Your Competent Partner for 
> > Computational Chemistry and Fluid Thermodynamics 




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From chemistry-request@server.ccl.net Tue Nov  5 10:59:09 2002
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From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf)
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Dear All,
I recently became a proud owner of Linux RedHat PC but now I am having 
few problems. I am trying to run DeepView (SwissProt Pdb viewer). I 
installed it without any errors but now when I try to run it I get a 
message:

"No response from any other spdbv process.
 Becoming master."

and screen comes up without any text.
Any idea what can be wrong here.
Thanks a lot for your help sorry to bother eveybody with this.
Mira

-- 
Miroslava Cuperlovic-Culf, Ph.D.
Research Scientist
Beausejour Medical Research Institute (IRMB)
Dr. Leon Richard Oncology Center
37 Providence Street
Moncton, NB E1C 8X3
Canada
fax: 506-862-4222
tel: 506-862-4848
e-mail: miroslavac@health.nb.ca 




From chemistry-request@server.ccl.net Tue Nov  5 15:08:57 2002
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Date: Tue, 05 Nov 2002 15:20:47 -0400
From: "Ronald R. Sauers" 
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Dear Folks:

I got an error message that I don't understand when attempting to
optimize the geometry of a conformer of an HBr:acetylene complex by a
method that worked for the original structure.  The molecule in question
has high symmetry:  Full point group = CS, Largest Abelian subgroup =
CS, and Largest Consise Abelian subgroup = CS.

The message was "Inconsistency #2 in MakNEB".

Can anyone tell me what this refers to and suggest a fix?

Thanks,

RRSauers


--

************************************************************************

Ronald R. Sauers                                732-445-2626 (office)
Professor Emeritus of Chemistry                 732-445-2618 (dept)
Department of Chemistry                         732-445-5312 (FAX)
Rutgers, The State University of New Jersey
610 Taylor Road
Piscataway, New Jersey 08854-8087 USA

E-mail:sauers@rutchem.rutgers.edu

************************************************************************




From chemistry-request@server.ccl.net Tue Nov  5 15:22:11 2002
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Date: Tue, 5 Nov 2002 23:19:35 +0300
From: Gregory Shamov 
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To: uccatvm 
CC: chemistry@ccl.net (CCL)
Subject: Re: CCL:Re:NWChem
In-Reply-To: <200211031355.gA3Dt9H12880@socrates-a.ucl.ac.uk>
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Hello uccatvm,

Sunday, November 3, 2002, 4:55:09 PM, you wrote:

u> It is true that NWChem is slower than Gaussian on a single processor.

Much much slower.

u>  However, the main advantage of NWChem is its, indeed, excellent
u> scalability, and that holds for small as well as large clusters,
u> for shared-memory as well as distributed-memory machines.
[skip]
u> As I mentioned above, as I do not have any experience with Gamess,
u> I cannot  comment on its performance on small clusters, but in my
u> experience NWChem  does scale very nicely on these machines.

NWChem scalability is not an advantage for small clusters, because
speed is sacrificed to it. What do you need from clusters -- smaller
wallclock times or better scalability? As I said, scalability of
NWChem is useful for large clusters only. 

Perhaps you better should try Gamess and double your calculation
speeds (not speedups).

u> In addition, because of its distributed data approach, it can
u> handle larger calculations on parallel machines where programs that
u> use a replicated-data approach

Yes, it is true. NWChem must be good for Grand Challenge tasks running
on Grand Size Clusters. (A propos, Gamess uses this DDI-thing for MP2
energies and gradients too).

u> This is very strange, because I don't see that behaviour. I get
u> very nice  speedups with NWChem, on small as well as larger
u> clusters. Running on 2  or 4 nodes, I generally get speedups of
u> close to 2 and 4 on different  architectures (that's for running ab
u> initio - like SCF and MP2 -  calculations). Even on Linux clusters
u> connected by only fast ethernet  I get speedups of 6.65 for running
u> on 4 dual processors. 

Today I have no working NWChem installation (because I have deleted it
year ago), but I will look for my old test results soon.

I have used (well, not used, just tested) NWChem on Linux clusters on
Alphas and PCs, with Fast and Gigabit Ethernet.

-- 
Best regards,
 Gregory                            mailto:gas5x@bancorp.ru



From chemistry-request@server.ccl.net Tue Nov  5 15:02:37 2002
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From: wei 
Reply-To: weiz@mail.rochester.edu
Organization: university of rochester
To: chemistry@ccl.net
Subject: help about charmm
Date: Tue, 5 Nov 2002 15:00:30 +0000
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Hi, all:

I want to use charmm to  minimize a big protein system(about 6600 atoms 
without exclude solvent). and in the output file, it said the following 
things about Nonbond properties. I am worrying about the statement "Maximum 
group spatial extent (12A) exceeded.Size is  15.85 Angstroms and starts with 
atom:    6046".

Is this serious? Do I have to do something or just let it be? 

Wei Zhuang

*****************************************************************************************
CHARMM>    NBONDS CUTNb 100.0 CTOFnb 99.0 CTONnb 98.0

 NONBOND OPTION FLAGS: 
     ELEC     VDW      ATOMs    CDIElec  SHIFt    VATOm    VSWItch 
     BYGRoup  NOEXtnd  NOEWald 
 CUTNB  =100.000 CTEXNB =999.000 CTONNB = 98.000 CTOFNB = 99.000
 WMIN   =  1.500 WRNMXD =  0.500 E14FAC =  1.000 EPS    =  1.000
 NBXMOD =      5
 There are        0 atom  pairs and        0 atom  exclusions.
 There are        0 group pairs and        0 group exclusions.
  with mode   5 found  19029 exclusions and  17626 interactions(1-4)
  found   5397 group exclusions.
 Generating nonbond list with Exclusion mode = 5
 VEHEAP> Expanding heap size by21954560 words.
 == PRIMARY == SPACE FOR 21826225 ATOM PAIRS AND        0 GROUP PAIRS
 NBONDA>>  Maximum group spatial extent (12A) exceeded.
   Size is       15.85 Angstroms and starts with atom:    6046
   Please check group boundary definitions.
***************************************************************************************8


From chemistry-request@server.ccl.net Tue Nov  5 18:24:40 2002
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From: "Benjamin T. King" 
To: 
Subject:  ZINDO, halogens, and g98
Date: Tue, 5 Nov 2002 14:53:15 -0800
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We are trying to use ZINDO, as implemented in g98 rev A.9, to estimate
the UV/VIS spectra for a variety of polyaromatic hydrocarbons.  This
works fine for unsubstituted hydrocarbons or chlorocarbons.  However, if
Br or I atoms are present, g98 crashes.  

We see two error messages:
	for a dibromobiphenyl, the error is:
	ZDOMap failed for IXNDO 4 -- possible missing parameters
	and
	for a bromoiodobiphenyl, the error is:
	IA out of range in SemiEx
Both errors occur in l301.

I suspect that the parameters for the heavier halogens were not included
in g98.  What needs to be done to include these parameters?  Has any
done this before, and if so, could they share their input files and
necessary modifications with us?  I believe that these parameters are
known - I have seen reports ZINDO spectroscopic calculations on
iodoarenes done using Cache (e.g. "Iodine-Benzene Charge-Transfer
Complex:  Potential Energy Surface and Transition Probabilities Studied
at Several Levels of Theory," Int. J. Quantum Chem, 1999, 75, 709-723.)

I will summarize responses and post what I learn.

Thank you,

Ben King

Benjamin T. King, Assistant Professor
Department of Chemistry/216
University of Nevada, Reno 89557
tel (775) 784-1736 fax (775) 784-6804
king@chem.unr.edu
http://www.chem.unr.edu/faculty/btk/ 


************************************

The input file for iodobromobiphenyl:
:
#P SP ZINDO Density

BROMOIODODBIPHENYL

0 1
 C    -0.575942     0.000000    -0.762986
 C     0.654559     0.000000     0.067573
 C     3.190745     0.000000     1.403142
 C     1.888004     0.000000    -0.615291
 C     0.774042     0.000000     1.463719
 C     2.004279     0.000000     2.119814
 C     3.120955     0.000000     0.016862
 H     1.916364     0.000000    -1.713368
 I    -0.690362     0.000000     2.815129
 H     2.050402     0.000000     3.216132
 H     4.038265     0.000000    -0.581692
 H     4.155501     0.000000     1.919889
 C    -2.997866     0.000000    -2.301536
 C    -1.853517     0.000000    -0.175193
 C    -0.601689     0.000000    -2.163709
 C    -1.760131     0.000000    -2.927091
 C    -3.030661     0.000000    -0.913942
 H    -1.997109     0.000000     0.903631
Br     0.890816     0.000000    -3.337786
 H    -1.697279     0.000000    -4.022011
 H    -3.994141     0.000000    -0.392059
 H    -3.921581     0.000000    -2.888309