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Date: Tue, 30 Jan 2001 08:21:49 -0500 (EST)
From: Peter Shenkin <shenkin@schrodinger.com>
To: chemistry@ccl.net
Subject: Re: CCL:An article worth reading
In-Reply-To: <Pine.GSO.3.95.1010129194525.16264B-100000@neon.chem.ucla.edu>
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Hi,

On Mon, 29 Jan 2001, Renxiao Wang wrote:

> .... I read a paper before, in which the author cited
> about 100 references. 60 or 70 of them are the previous work of his own
> and here is how he cited them (something like that): "we have also applied
> this method to other systems [20-80], ...". Ooops. 
> 
> So what do you say?

I say, "See my previous postings in CCL for further comments."

:-),
-P.



From chemistry-request@server.ccl.net Tue Jan 30 11:49:44 2001
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 30 Jan 2001 11:51:45 EDT
Date: Tue, 30 Jan 2001 11:51:45 -0400 (EDT)
From: srhughes@vax2.concordia.ca
Subject: BBSE corrections
To: CCL <chemistry@ccl.net>
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Hello CCLers,

Are there circumstances under which it is possible to have an increase in
energy after employing a counterpoise BSSE correction?  Over the course
of my calculations, I am consistently obtaining higher energies after
corrections are applied.  The system I am studying includes an ECP (SDD
large core) and a Pople basis set (6-31+G(2d,p).  Is it possible that the
use of a mixed basis set may affect the correction?  I have not seen this
anywhere and, instinctively, I would assume that as basis sets are added
to a system, the resultant energy should be lowered.  

Thank you for your time.

Sean Hughes
Centre for Research in Molecular Modeling (CERMM)
Dept. Chemistry and Biochemistry
Concordia University
1455 de Maisonneuve Blvd. West
Montreal, Quebec
Canada
H3G 1M8
Tel: (514)-848-4260
Fax: (514)-848-2868   


From chemistry-request@server.ccl.net Tue Jan 30 09:29:14 2001
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Subject: 2001.03.20-23 MSI Customer Training Workshops in York, UK
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Molecular Simulations Inc. will be holding a pair of 2-day workshops 
involving Cerius2 at the University of York, York, UK.

On 20-21 March, the "Introduction to Cerius2 for Life Sciences Workshop" 
will be offered.  This course provides an overview of molecular modeling 
techniques for life sciences applications using Cerius2.  The workshop will 
focus on basic skills for use of the interface and will explore various 
modules in the areas of rational-drug design, structure-based drug design, 
and combinatorial chemistry.  Prior modeling experience is not assumed 
making this course a great place to learn molecular modeling with Cerius2.

On 22-23 March, the "Combinatorial Chemistry" workshop will be 
offered.  This workshop is an introduction to library design and analysis 
in combinatorial techniques using the Cerius2 interface.  Attendees should 
have a basic understanding of QSAR theory and either extensive experience 
with Cerius2 or completion of the "Introduction to Cerius2 for Life 
Sciences Workshop".

Fees for each 2-day course are GBP 700 commercial, GBP 350 government, and 
GBP 280 academic.  However, register for both courses and receive a 25% 
discount for the second course.

Further detailed information about this and other MSI training workshops, 
as well as on-line course registration, can be found at MSI's website 
(http://www.msi.com/about/events/training).  Please do not hesitate to 
contact us should you have any questions.

Thank you very much.

				Jeffrey L. Nauss
				MSI Customer Training Programs

--
Jeffrey L. Nauss, PhD		Phone: (858) 799-5555
Customer Training Programs	Fax: (858) 458-0136
Molecular Simulations Inc.	E-mail: jnauss@msi.com
9685 Scranton Road		http://www.msi.com/about/events/training
San Diego, CA 92121-3752



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Date: Tue, 30 Jan 2001 04:31:00 -0500
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From: Jeff Nauss <jnauss@msi.com>
Subject: 01.03.27 MSI Customer Training Workshops on Catalyst
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The week before the 221st American Chemical Society National meeting, 
Molecular Simulations Inc. will be holding a pair of 2-day workshops at the 
San Diego Supercomputer Center, San Diego, CA.  These workshops will 
involve the Catalyst user interface.

On March 27-28, the "Introduction to Catalyst Workshop" will be 
presented.  This workshop is intended to introduce customers to 
pharmacophore generation and to the Catalyst user interface. No prior 
experience with molecular modeling is needed. The workshop begins with the 
basics of the Catalyst interface and builds to simple pharmacophore 
generation, selection of training sets, and three-dimensional database 
searching.

The "Advanced Pharmacophore and 3D Database Searching Techniques Workshop" 
will be presented on March 29-30.  This workshop is for advanced users who 
are interested in how to best exploit the most useful features within 
Catalyst.  Methods used within Catalyst for automatic hypothesis generation 
and manual hypothesis construction will be discussed.  Optimization of 
training sets and database searching will be covered as well.  Successful 
strategies and techniques to take advantage of these methods will also be 
presented

These workshops are to provide attendees with the Catalyst-eye view of the 
structure-activity world that is necessary to best exploit its most useful 
features.  Lectures presenting the methodologies and examples of their 
application to solve real-world problems will be followed by 
hands-on/discussion periods during which attendees can work though 
tutorials or discuss their own work with experts from MSI.

Attendees should possess knowledge of basic UNIX commands and have a basic 
understanding of QSAR theory.  Attendees for the advanced workshop should 
have either experience with Catalyst or have completed the "Introduction to 
Catalyst Workshop."

Fees for the 2-day course are $1000 commercial, $500 government, and $400 
academic.  Register for both workshops and receive a 25% discount on the 
second workshop.

Further detailed information about this and other MSI training workshops, 
as well as on-line course registration, can be found at MSI's website 
(http://www.msi.com/about/events/training).  Please do not hesitate to 
contact us should you have any questions.

Thank you very much.

				Jeffrey L. Nauss
				858-799-5555

				Chris Arzt
				858-799-5340

--
Jeffrey L. Nauss, PhD		Phone: (858) 799-5555
Customer Training Programs	Fax: (858) 458-0136
Molecular Simulations Inc.	E-mail: jnauss@msi.com
9685 Scranton Road		http://www.msi.com/about/events/training
San Diego, CA 92121-3752



From chemistry-request@server.ccl.net Tue Jan 30 13:37:18 2001
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Date: Tue, 30 Jan 2001 12:37:12 -0600 (CST)
From: TREVOR D POWER <tdp0006@unt.edu>
To: chemistry@ccl.net
Subject: Re: CCL:BBSE corrections
In-Reply-To: <Pine.PMDF.3.96.1010130113647.693339B-100000@vax2.concordia.ca>
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Sean,
	To respond to your first question: It really depends where you are
on the potential energy surface when you apply the conterpoise correction
method.  Note that the minimum obtained from a geometry optimization
(where BSSE correction is necessary) results from the unphysical
interaction between orbitals (occupied and unoccupied) of monomer A and B.
This unphysical interaction of orbitals places the optimized geometry such
that monomers A and B are closer than they should be.  If this equilibrium
point is where you apply the counterpoise correction method, you will find
that the BSSE corrected energies are higher than they were before the
correction was applied.  

Hope this helps,
David Power
Department of Chemistry
University of North Texas
NT Station, Box 305070
Denton, Texas 76203-5070
tdp0006@unt.edu

On Tue, 30 Jan 2001 srhughes@vax2.concordia.ca wrote:

> Hello CCLers,
> 
> Are there circumstances under which it is possible to have an increase in
> energy after employing a counterpoise BSSE correction?  Over the course
> of my calculations, I am consistently obtaining higher energies after
> corrections are applied.  The system I am studying includes an ECP (SDD
> large core) and a Pople basis set (6-31+G(2d,p).  Is it possible that the
> use of a mixed basis set may affect the correction?  I have not seen this
> anywhere and, instinctively, I would assume that as basis sets are added
> to a system, the resultant energy should be lowered.  
> 
> Thank you for your time.
> 
> Sean Hughes
> Centre for Research in Molecular Modeling (CERMM)
> Dept. Chemistry and Biochemistry
> Concordia University
> 1455 de Maisonneuve Blvd. West
> Montreal, Quebec
> Canada
> H3G 1M8
> Tel: (514)-848-4260
> Fax: (514)-848-2868   
> 
> 
> -= This is automatically added to each message by mailing script =-
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> 
> 
> 
> 
> 
> 


From chemistry-request@server.ccl.net Tue Jan 30 18:40:52 2001
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	Tue, 30 Jan 2001 15:40:41 -0800
Date: Tue, 30 Jan 2001 15:40:36 -0800 (PST)
From: Roy Jensen <royj@UVic.CA>
To: <chemistry@ccl.net>
Subject: Transition State Optimization
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All

I am attempting a transition state optimization on G98W A.9, currently on
HOCN. Using a multitude of methods, basis sets, and starting geometries,
I fail to get a negative eigenvalue after the first step. The exact error:
	-- Wrong number of Negative eigenvalues: Desired=  1 Actual=  0

Has anyone experienced this problem?
An input file is copied below.

Roy Jensen


===========================
#P MP2/6-31G opt(TS) nosymm

Transition state optimization for HOCN.

0 1
H
O 1 R1
C 2 R2 1 A1
N 2 R3 3 A2 1 D1

R1=0.97
R2=1.20
R3=1.20
A1=115.
A2=125.
D1=179.999



From chemistry-request@server.ccl.net Tue Jan 30 18:49:35 2001
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Date: Tue, 30 Jan 2001 15:49:33 -0800 (PST)
From: Roy Jensen <royj@UVic.CA>
To: <chemistry@ccl.net>
Subject: SLATERDET keyword in Gaussian 98
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I am trying to find a singlet-triplet crossing.

Has anyone sucessfully used the SLATERDET keyword to accomplish this?
Are there any other ways to estimate the crossing?

Thanks,
Roy Jensen



From chemistry-request@server.ccl.net Tue Jan 30 19:09:03 2001
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From: "Stefan Fau" <fau@qtp.ufl.edu>
To: "Roy Jensen" <royj@UVic.CA>
Cc: "CCL - all" <CHEMISTRY@ccl.net>
References: <Pine.A41.4.30.0101301526190.22452-100000@unix4.UVic.CA>
Subject: Re: CCL:Transition State Optimization
Date: Tue, 30 Jan 2001 19:12:45 -0500
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Hi Roy,

the error message means that the approximate
hessian used in the geometry/TS optimization has no
negative eigenvalue, i.e. you are far from the TS. If
you do not calculate force constants [opt(calcfc)] or
read them from the checkpointfile [opt(readfc)], a
rougher hessian will be provided from some empirical
rules and/or a force field. That does not necessarily
work well for transition states. Try opt(calcfc,ts) or
opt(calchffc,ts).

Opt=ts is the best method if your starting geometry
is relatively close to the TS geometry. If you have only
a vague idea of the TS geometry, opt(qst3) works well.
You have to specify the geometries of reactant, product
and TS-guess with the same sequence of atoms. This
method is good for getting close to the TS. It may be
slower than opt(ts) once you are close to the TS.

For details with the keywords, look at
http://www.gaussian.com/techinfo.htm

Stefan
______________________________________________________________________
Dr. Stefan Fau                    |      fau@qtp.ufl.edu
Quantum Theory Project     |     (352) 392-6714
University of Florida
Gainesville, FL 32611-8435


From chemistry-request@server.ccl.net Tue Jan 30 19:32:08 2001
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Date: Tue, 30 Jan 2001 18:32:04 -0600 (CST)
From: TREVOR D POWER <tdp0006@unt.edu>
To: chemistry@ccl.net
Subject: Re: CCL:Transition State Optimization
In-Reply-To: <Pine.A41.4.30.0101301526190.22452-100000@unix4.UVic.CA>
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Roy,
	The easiest thing to do is specify opt=(NoEigenTest,TS) in the
route card.  I have been locating transition states for over 5 years and I
have NEVER found one with just opt=TS.  QST3 has a lot of bugs.  For
instance, several times I have set this up and the job actually converges
but the program will just iterate to a new optimization cycle.  You really
have to pay attention to the output or the job may never seem to terminate
properly.

Cheers,
David Power
Department of Chemistry
University of North Texas
NT Station, Box 305070
Denton, Texas 76203-5070
tdp0006@unt.edu

On Tue, 30 Jan 2001, Roy Jensen wrote:

> All
> 
> I am attempting a transition state optimization on G98W A.9, currently on
> HOCN. Using a multitude of methods, basis sets, and starting geometries,
> I fail to get a negative eigenvalue after the first step. The exact error:
> 	-- Wrong number of Negative eigenvalues: Desired=  1 Actual=  0
> 
> Has anyone experienced this problem?
> An input file is copied below.
> 
> Roy Jensen
> 
> 
> ===========================
> #P MP2/6-31G opt(TS) nosymm
> 
> Transition state optimization for HOCN.
> 
> 0 1
> H
> O 1 R1
> C 2 R2 1 A1
> N 2 R3 3 A2 1 D1
> 
> R1=0.97
> R2=1.20
> R3=1.20
> A1=115.
> A2=125.
> D1=179.999
> 
> 
> 
> -= This is automatically added to each message by mailing script =-
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> MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH
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> 
> 
> 
> 
> 
> 


From chemistry-request@server.ccl.net Tue Jan 30 19:28:30 2001
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Message-ID: <00d101c08b1c$94d36140$25037b81@tapaskar>
From: "Tapas Kar" <tapaskar@cc.usu.edu>
To: "Roy Jensen" <royj@UVic.CA>, <chemistry@ccl.net>
References: <Pine.A41.4.30.0101301526190.22452-100000@unix4.UVic.CA>
Subject: Re: CCL:Transition State Optimization
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Use NoEigenTest keyword.
_______________________________________

Tapas Kar, Ph.D
Department of Chemistry & Biochemistry
Utah State University
0300 Old Main Hill
Logan, UT 84322-0300

Voice: 435-797-7230
Fax:   435-797-3390
Email: tapaskar@cc.usu.edu
       tapas@risky3.chem.usu.edu

-----------------------------------------
----- Original Message -----
From: "Roy Jensen" <royj@UVic.CA>
To: <chemistry@ccl.net>
Sent: Tuesday, January 30, 2001 4:40 PM
Subject: CCL:Transition State Optimization


> All
>
> I am attempting a transition state optimization on G98W
A.9, currently on
> HOCN. Using a multitude of methods, basis sets, and
starting geometries,
> I fail to get a negative eigenvalue after the first step.
The exact error:
> -- Wrong number of Negative eigenvalues: Desired=  1
Actual=  0
>
> Has anyone experienced this problem?
> An input file is copied below.
>
> Roy Jensen
>
>
> ===========================
> #P MP2/6-31G opt(TS) nosymm
>
> Transition state optimization for HOCN.
>
> 0 1
> H
> O 1 R1
> C 2 R2 1 A1
> N 2 R3 3 A2 1 D1
>
> R1=0.97
> R2=1.20
> R3=1.20
> A1=115.
> A2=125.
> D1=179.999
>
>
>
> -= 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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gopher.ccl.net 70
> Ftp: ftp.ccl.net  |  WWW: http://www.ccl.net/chemistry/
| Jan: jkl@ccl.net
>
>
>
>
>




From chemistry-request@server.ccl.net Tue Jan 30 22:08:01 2001
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Date: Tue, 30 Jan 2001 21:08:01 -0600 (CST)
From: Ohyun Kwon <kwonohy@auburn.edu>
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To: Roy Jensen <royj@uvic.ca>
cc: chemistry@ccl.net
Subject: Re: CCL:Transition State Optimization
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Dear Roy;
Try to use option like ;
# opt=(ts,calcfc,noeigentest)

"noeigentest" indicate program to skip the test of number of negative
eigenvalue.
Good luck.

Tommy Kwon

On Tue, 30 Jan 2001, Roy Jensen wrote:

> All
> 
> I am attempting a transition state optimization on G98W A.9, currently on
> HOCN. Using a multitude of methods, basis sets, and starting geometries,
> I fail to get a negative eigenvalue after the first step. The exact error:
> 	-- Wrong number of Negative eigenvalues: Desired=  1 Actual=  0
> 
> Has anyone experienced this problem?
> An input file is copied below.
> 
> Roy Jensen
> 
> 
> ===========================
> #P MP2/6-31G opt(TS) nosymm
> 
> Transition state optimization for HOCN.
> 
> 0 1
> H
> O 1 R1
> C 2 R2 1 A1
> N 2 R3 3 A2 1 D1
> 
> R1=0.97
> R2=1.20
> R3=1.20
> A1=115.
> A2=125.
> D1=179.999
> 
> 
> 
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