From gford@post.smu.edu  Wed Sep 25 10:57:48 1996
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Date: Wed, 25 Sep 96 09:37 CDT
From: "George P. Ford"  <gford@post.smu.edu>
Reply-To: "George P. Ford"  <gford@mail.smu.edu>
To: CHEMISTRY@www.ccl.net
Subject: Tripos 5.2 force field (Sybyl)


Can anybody tell me what modeling packages include an implementation of the 
Tripos 5.2 force field, (Clark et al, J. Comp. Chem., 1989, 10, 982) as either 
part of a builder, or as a bona fide minimizer? I already know about, Sybyl, 
Alchemy, and Spartan.

George P. Ford





============================================================================
George P. Ford                          |       email:  gford@smu.edu
Department of Chemistry                 |   telephone:  (214)768-2479
Southern Methodist University           |         fax:  (214)768-4089
Dallas, Texas 75275                     |        http://www.smu.edu/~gford/
============================================================================
   


From hocquet@cas.lca.espci.fr  Wed Sep 25 12:57:46 1996
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To: chemistry@www.ccl.net
From: hocquet@cas.lca.espci.fr (Alexandre Hocquet)
Subject: what is what if ?


dear cclers,
i recently heard about a molecular graphics software called WHAT IF
>from academic people in Heildeberg (or nearby...)
could someone describe its capabilities and ways of obtaining it ?

thanks in advance

A. Hocquet
espci
chimie analytique
10, rue Vauquelin
75231 Paris c=E9dex 05
France


From owner-chemistry@ccl.net  Wed Sep 25 13:00:49 1996
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From: markm@portal.vpharm.com (Mark Murcko)
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Subject: Benchmarks
To: chemistry@ccl.net
Date: Wed, 25 Sep 1996 10:40:39 -0500 (EDT)
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Dear CCL number-crunchers!

We are considering the purchase of a new computer for large-
scale simulations.  Mostly AMBER, XPLOR, and GAUSSIAN.  I
am looking for benchmarks and other hard data comparing the
following processors: the DEC alpha 440 MHz, the IBM 120 MHz,
and the SGI R10K.  Data showing the performance of these chips
for typical chemistry applications would be greatly appreciated.
Data for the previous-generation chips would be useful too
(e.g. the IBM 67 MHz or 77 MHz, the DEC 350 MHz, etc.).
Information about 4-way and 8-way parallel performance would
also be great, if any exists.  Experiences with the stability
of hardware, O/S, and compilers also welcome.  Thanks!

/ Mark Murcko
Vertex Pharmaceuticals

From hutschka@quantix.u-strasbg.fr  Wed Sep 25 13:01:59 1996
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Date: Wed, 25 Sep 1996 17:27:52 +0200
Message-Id: <9609251527.AA55255@quantix.u-strasbg.fr>
To: chemistry@www.ccl.net
Subject: Correlation effect on calc atomic Charges
Cc: hutschka@quantix.u-strasbg.fr



Hello,

I'm calculating atomic charges with Gaussian using Mulliken population
analysis and fitting to electrostatic potential methods.
I've noted some important differences between Mull and ESP derived charges.
More , for ESP derived charges the use of correlated densities (MP2 density in this case)
gives important differences with the use of HF density.
So I would like to know if someone could advise me some references (review article would
be nice) about the comparison of this methods and about the effect of correlation
on the caculated charges.
Another question : Does it make sense to do a Mulliken population analysis with the MP2
density ??
Any comment or help is welcome.
Results will be summarized for everybody.
Thanks.

=============================================================================
¤  François HUTSCHKA                 Ph.D. Student in Quantum Chemistry     ¤
¤                                                                           ¤
¤  Laboratoire de Chimie Quantique                                          ¤
¤  UPR 139 du CNRS                                                          ¤
¤  4, rue Blaise Pascal              Phone:  (33).88.41.60.32               ¤
¤  67000 STRASBOURG                  Fax:    (33).88.61.20.85               ¤
¤  FRANCE                            E-Mail: hutschka@quantix.u-strasbg.fr  ¤
=============================================================================


From dimitris@3dp.com  Wed Sep 25 13:57:49 1996
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Date: Wed, 25 Sep 1996 13:49:20 -0400
In-Reply-To: hocquet@cas.lca.espci.fr (Alexandre Hocquet)
        "CCL:what is what if ?" (Sep 25,  5:29pm)
References: <9609251529.AA15534@cas.lca.espci.fr>
X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail)
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Subject: Re: CCL:what is what if ?
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It's a rather extensive sequence analysis package from EMBL. For more
info, have a look at:

http://www.sander.embl-heidelberg.de/whatif/

Hope that helps.

-- 
Dimitris K. Agrafiotis, PhD              | e-mail: dimitris@3dp.com
3-Dimensional Pharmaceuticals, Inc.      | tel:    (610) 458-6045
665 Stockton Drive, Suite 104            | fax:    (610) 458-8249
Exton, PA 19341


From raman@bioc01.uthscsa.edu  Wed Sep 25 14:00:35 1996
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Date: Wed, 25 Sep 1996 12:15:00 -0500 (CDT)
From: raman@bioc01.uthscsa.edu (C.S.RAMAN)
Subject: Re: CCL:what is what if ?
In-reply-to: <9609251529.AA15534@cas.lca.espci.fr>
To: hocquet@cas.lca.espci.fr (Alexandre Hocquet)
Cc: chemistry@www.ccl.net
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Alexandre:

> i recently heard about a molecular graphics software called WHAT IF
> from academic people in Heildeberg (or nearby...)
> could someone describe its capabilities and ways of obtaining it ?

WHAT IF is a complete macrmolecular modelling program and can be
obtained from Dr. Gerrit Vriend, EMBL, Heidelberg.  You can contact him
at :  vriend@embl-heidelberg.de

Cheers
-raman
______________________________________________________________________
C.S.Raman                              Tel: (210) 614-0839
Dept. of Biochemistry                  Fax: (210) 567-2490
University of Texas                    email:raman@bioc01.uthscsa.edu
Health Science Center
7703 Floyd Curl Drive                     
San Antonio, TX, 78284-7760  U.S.A.
----------------------------------------------------------------------
     The real problem in speech is not precise language.  
     The problem is clear language. --Richard Feynman
______________________________________________________________________

From owner-chemistry@ccl.net  Wed Sep 25 14:57:51 1996
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Date: Wed, 25 Sep 1996 11:27:47 +42000
From: Konstantin Momot <momot@iris5.chem.Arizona.EDU>
Subject: Spartan from remote terminal
To: Computational Chemistry List <CHEMISTRY@ccl.net>
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Hello everybody,

Has anyone started a Spartan job in the background from a remote 
non-graphics terminal?  I tried, and here's the outcome:

When I try 

/usr3/spartan4.0_405/sp_abinitio fe_nh3_6_tetrag &

it complaints that env. var. SPAR_ACCESS is undefined. When I define the 
variable:

        setenv SPAR_ACCESS /usr3/spartan4.0_405

and start it again, the job starts, but is immediately suspended with the 
following message:


SPARTAN AB INITIO PROGRAM:  SGI/IRIX4  Release 4.0.1a
  (Job run on iris3)

[1]  + Stopped (tty input)  /usr3/spartan4.0_405/sp_abinitio fe_nh3_6     


Obviously, files _spartan, input, and propin are present in /fe_nh3_6 
when I attempt to start the job.  Does anyone know why would it wait for 
standard input and how to avoid it ? 

Thanks in advance for your suggestions; I will post the solution to the 
problem on the list.

--

Konstantin Momot

momot@iris5.chem.arizona.edu      
http://aruba.ccit.arizona.edu/~momot/research.html     



From hinsen@ibs.ibs.fr  Wed Sep 25 15:00:24 1996
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Date: Wed, 25 Sep 96 20:19:42 +0100
From: Konrad Hinsen <hinsen@ibs.ibs.fr>
To: hutschka@quantix.u-strasbg.fr
Cc: chemistry@www.ccl.net
In-Reply-To: <9609251527.AA55255@quantix.u-strasbg.fr>
	(hutschka@quantix.u-strasbg.fr)
Subject: Re: CCL:G:Correlation effect on calc atomic Charges


> I'm calculating atomic charges with Gaussian using Mulliken population
> analysis and fitting to electrostatic potential methods.

You didn't say *why* you are doing this, so I assume that the goal
is obtaining partial charges for an empirical force field.

> I've noted some important differences between Mull and ESP derived charges.
> More , for ESP derived charges the use of correlated densities (MP2 density in this case)
> gives important differences with the use of HF density.

First of all, Mulliken charges are based on a somewhat arbitrary
assignment of parts of electron densities to the individual atoms.
They may give some indication of polarization etc., but as a source
for partial charge information they are not very useful.

ESP-derived charges depend on
1) the ab-initio reference potential (which includes basis-set dependence)
2) the choice of evaluation points for the potential
3) the method used for fitting the charges.

Dependence 1) is obvious and if you find that your charges depend on
the level of calculation (provided that you haven't done something
stupid regarding 2) and 3)), then this is a feature of your system
that you have to understand and draw conclusions from. The dependence
on the evaluation points is equally obvious, but there is no single
choice that everyone agrees on (and to some extent it depends on
what you want to do with the fitted charges). Among the strategies
that have been proposed are:
1) points on a grid around the molecule (not recommendable due to
   the dependence on arbitrary grid axes)
2) points on well-defined surfaces around the molecule
3) points chosen at random in a well-defined region around the
   molecule.

Dependence 3) is more problematic, since it shouldn't be there in an
ideal world. The proposed methods differ in numerical stability and in
the exact quantity they are trying to minimize. Basically, everyone
agrees that what we want is a least-squares fit. Such fits are in
general known to be problematic, because the solution is often
underdetermined, and this also occurs for charge fitting. It is
therefore *not* a good idea to simply solve the normal equations for
the least-squares, but unfortunately that is what most people are
doing. A much safer alternative is singular-value decomposition, as
described in most books on matrix computations, or even in the second
edition of Numerical Recipes.

Beyond the problem of numerical stability of the fit, one popular
method (known as RESP) proposes to put a constraint on the absolute
value of the charges, based on the observation that ESP often gives
charges that seem to large. I don't know in how far this is a result
of numerical instabilities (RESP does not use singular value
decomposition) or of some real physical effect; this ought to be
investigated.

Literature:

C.I. Bayly, P. Cieplak, W.D. Cornell and P.A. Kollman
J. Phys. Chem. 97, 10269 (1993)
(This paper describes RESP.)

K. Hinsen and B. Roux
J. Comp. Chem., in print  (contact me for a preprint)
(This paper describes a specific potential function for proton transfer
simulations, but contains an extensive appendix that describes a
charge-fitting strategy based on singular-value decomposition.)

Both papers contain references to older methods. There is another
paper that has appeared earlier this year in J. Comp. Chem. and which
deals explicitly with an SVD-based fitting method, but I haven't
seen it yet.

-------------------------------------------------------------------------------
Konrad Hinsen                          | E-Mail: hinsen@ibs.ibs.fr
Laboratoire de Dynamique Moleculaire   | Tel.: +33-76.88.99.28
Institut de Biologie Structurale       | Fax:  +33-76.88.54.94
41, av. des Martyrs                    | Deutsch/Esperanto/English/
38027 Grenoble Cedex 1, France         | Nederlands/Francais
-------------------------------------------------------------------------------

From owner-chemistry@ccl.net  Wed Sep 25 15:57:54 1996
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 25 Sep 1996 13:04:06 -0700
Date: Wed, 25 Sep 1996 13:04:05 +42000
From: Konstantin Momot <momot@iris5.chem.Arizona.EDU>
Subject: Spartan: PURED keyword ?
To: Computational Chemistry List <CHEMISTRY@ccl.net>
Message-id: <Pine.SGI.3.90.960925125334.2840A-100000@iris5.chem.Arizona.EDU>
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Hi everybody,

here's another question about Spartan.  I am trying to use PURED keyword 
which is supposed to define d-functions as the five (real) spherical AOs 
rather than the six Cartesian functions.

On Fe atom, the keyword works with the STO-3G basis set, but not with the 
3-21G* set.  Could I be doing something wrong ?  And why does the keyword 
work differently with different basis sets ?  

Any ideas, solutions etc. will be appreciated.  I will summarize and post 
the replies.

--

Konstantin Momot

momot@iris5.chem.arizona.edu        
http://aruba.ccit.arizona.edu/~momot/research.html 



From huang@nissan.wavefun.com  Wed Sep 25 17:57:48 1996
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From: "Wayne Huang" <huang@nissan.wavefun.com>
Message-Id: <9609251351.ZM17153@nissan.wavefun.com>
Date: Wed, 25 Sep 1996 13:51:44 -0700
In-Reply-To: Alan.Shusterman@directory.Reed.EDU (Alan Shusterman)
        "CCL:Spartan from remote terminal" (Sep 25,  1:13pm)
References: <1748569@isis.Reed.EDU>
Reply-To: huang@wavefun.com
X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail)
To: momot@iris5.chem.Arizona.EDU
Subject: Re: CCL:Spartan from remote terminal
Cc: chemistry@www.ccl.net
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii



> >Date: Wed, 25 Sep 1996 11:27:47 +42000
> >From: Konstantin Momot <momot@iris5.chem.Arizona.EDU>
> >Subject: CCL:Spartan from remote terminal
> >To: Computational Chemistry List <CHEMISTRY@ccl.net>
>
> Hello everybody,
>
> Has anyone started a Spartan job in the background from a remote
> non-graphics terminal? ...

Konstantin,

Spartan jobs can be launched without Spartan GUI via non-graphical terminals
such as ascii terminals or home computers with modem. Here is how it works:

(1) remote login to unix workstation with Spartan on it;

(2) Go to the directory where the molecule (e.g. test) locates;

(3) type in 'spartan -x test &' which allows the pre-set job to run, you could
    certainly modify the input file with text editor for different setup
    options, or other text-only modification,

(4) Check the progress of your job by 'ps -ef|grep spartan'.

Hope this answer the question.

--Wayne



-- 
+---------------------------------------------------------------+
|  Wayne Huang, Ph.D.    	|  18401 Von Karman, Suite 370  | 
|  Computational Chemist 	|  Irvine, California 92715     |
|  Wavefunction, Inc.    	|  714-955-2120 <> 955-2118(fax)|  
|  huang@wavefun.com     	|  Web: http://www.wavefun.com  |
+---------------------------------------------------------------+



From li@pink.incm.u-nancy.fr  Wed Sep 25 18:04:54 1996
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Date: Wed, 25 Sep 1996 23:01:58 +0100 (EDT)
From: G-S LI <li@pink.incm.u-nancy.fr>
To: hutschka@quantix.u-strasbg.fr
cc: chemistry@www.ccl.net
Subject: Re: CCL:G:Correlation effect on calc atomic Charges
In-Reply-To: <9609251527.AA55255@quantix.u-strasbg.fr>
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Fran=E7ois,

    For a good review, see=20

S.M.Bachrach, "Population analysis and electron densities from quantum=20
mechanics", in Reviews in Computational Chemistry, Vol.V, eds.=20
K.B.Lipkowitz and D.B.Boyd, VCH publishers, Inc. New York, 1994, Chap.3.=20
p.171-227.

    You may also refer to a recent paper:

S.Tsuzuki et al., " Comparison of atomic charge distributions obtained=20
>from different procedures: basis set and electron correlation effects",=20
J. Mol. Struc.(Theochem), 365(1996),81-88.

    By the way, your interest is on "single-bonded" systems or=20
"multiple-bonded" systems, and on isolated molecules or complex ?
Electron correlation may have different effects on them. As for the=20
former point, I agree with Bachrach's opinion, i.e. the effect of
electron correlation on atomic populations is quite small for single-
bonded systems, while much more substantial for multiple-bonded systems.=20
For complex, situations are much more difficult and according to my=20
experience, no one procedure can be satisfactory in most of the cases.=20
(Hope this is not true !)

    Hope you will have some new findings.

Guosheng LI
Lab. de Chimie Theorique
Univ. de Nancy-I
li@pink.incm.u-nancy.fr

>=20
> Hello,
>=20
> I'm calculating atomic charges with Gaussian using Mulliken population
> analysis and fitting to electrostatic potential methods.
> I've noted some important differences between Mull and ESP derived charge=
s.
> More , for ESP derived charges the use of correlated densities (MP2 densi=
ty in this case)
> gives important differences with the use of HF density.
> So I would like to know if someone could advise me some references (revie=
w article would
> be nice) about the comparison of this methods and about the effect of cor=
relation
> on the caculated charges.
> Another question : Does it make sense to do a Mulliken population analysi=
s with the MP2
> density ??
> Any comment or help is welcome.
> Results will be summarized for everybody.
> Thanks.
>=20
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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> =A4  Fran=E7ois HUTSCHKA                 Ph.D. Student in Quantum Chemist=
ry     =A4
> =A4                                                                      =
     =A4
> =A4  Laboratoire de Chimie Quantique                                     =
     =A4
> =A4  UPR 139 du CNRS                                                     =
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> =A4  4, rue Blaise Pascal              Phone:  (33).88.41.60.32          =
     =A4
> =A4  67000 STRASBOURG                  Fax:    (33).88.61.20.85          =
     =A4
> =A4  FRANCE                            E-Mail: hutschka@quantix.u-strasbg=
 .fr  =A4
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
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