Subject: Re: G: Gaussian Frequency calculation

From: "Jens Spanget-Larsen" <[email-masked]>
Date: Fri, 4 Jul 1997 11:06:00 +0100

Dale:

On 2 Jul 1997, you wrote: 07:36:12 -0700 (PDT)

> If you get a response to this question, please post it to the CCL or G; I
> am very interested in hearing the answer, as I have wondered about the
> validity of Rupert's claim myself.  I don't understand why people write
> their own routines to diagonalize the full force-constant matrix provided
> by G94, when it would be much simpler to just mass-weight the
> eigenvectors, and renormalize.

As you may have gathered from the postings on the G-list, the 
discussion is continuing.  It turns out that the 'proper' 
cartesian displacement coefficients are obtained from the printed 
G94 normal mode coefficients in the following way:

MULTIPLY THE PRINTED G94 NORMAL MODE COEFFICIENTS BY THE INVERSE
SQUARE ROOT OF THE REDUCED MASS 'M'. 

This produces the cartesian displacement vector X in 'real' x-space, 
that corresponds to a normal mode vector Q of unit length in 
abstract, mass-weighted q-space.  It is as simple as that, and you 
have the following relation between the length of the two vectors:
|Q| = sqr(M)|X|.

This, of course, should be well known by a lot of people (?), but I 
had to find it out by myself.  John Bertie <[email-masked]> 
has recently worked it all out in formal matrix algebra.

Another problem: You suggest a posting on the CCL, but my recent 
attempts to submit messages to CCL <[email-masked]> 
have been without effect: I get no mail error messages, but my 
messages don't appear on the list!  What may be wrong?

I am out of town for the next two weeks. 

Jens >--< 

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=
JENS SPANGET-LARSEN  
Department of Chemistry      Phone:  +45 46757781 + 2710
Roskilde University (RUC)    Fax:    +45 46757721 
P.O.Box 260                  E-Mail: [email-masked]
DK-4000 Roskilde, Denmark    http://frederik.ruc.dk/dis/chem/psos
=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

>From [email-masked] Thu Jul  3 12:19 EDT 1997
Date: Thu, 3 Jul 1997 10:22:49 -0600
To: [email-masked]
From: [email-masked] (Michael Page)
Subject:  ACS THEORY/IBM grad student computer awards - call for Apps.
Cc: [email-masked]
Content-Length: 2602
Status: RO

 --Call for Applicants

IBM Graduate Student Awards in Computational Chemistry

Below is an announcement for two Awards in Computational  Chemistry that
are open to current graduate students.   We are grateful to  IBM and the
Minnesota Supercomputing Institute for their support of these awards.

Let me urge you to encourage your graduate students to apply.  The
competition is open to any graduate student (regardless of  citizenship)
who began graduate study after August 1, 1994 and who is an ACS member (or
whose advisor is an ACS  member).  These awards are designed to encourage
graduate work in stimulate interest in the Subdivision of Theoretical
Chemistry
and the Physical Chemistry Division of the ACS.
An Awards Committee will consider all the applicants. The awards
applications should be sent to Professor Bill Hase at Wayne State University.
Note that the deadline for applications is August 15.

These two awards,  supported by IBM, will provide one-time cash stipends
of $2500 and $1000 as supplements to normal
financial aid to  doctoral candidates in the research-dissertation  stage
in the 1997-1998 academic year.  The Minnesota Supercomputing Institute
will  provide each awardee up to 1000 node-hours on an IBM SP2 cluster for
the awardees to actually carry out a portion of the awarded  research.  The
awardees will have access to the consulting services  of the Institute
normally available to all users.  Awardee selection will be made on a
competitive basis.  Applicants should be working on new and innovative
computational  chemistry methods or applications in theoretical chemistry.

Applicants should prepare a written description of a  computational
chemistry research project that requires high  performance computing, with
an explanation of the scientific  importance of the project. Proposals need
to include an estimate  of the computing resources required in SP2
cpu-hours.  Applicants  should explain how they plan to use the grant
funds.  Two letters  of recommendation, including one from the student's
advisor, along  with a vita and transcript, are required. The proposal,
including the vita,  should not exceed five double-spaced pages. In
addition, a faculty person (typically the applicant's research advisor)
responsible for the applicant's use of the Minnesota Supercomputing
Institute resources must be identified.

Forward applications by  August 15, 1997 to

Prof. Bill Hase
Department of Chemistry
Wayne State University
Detroit, MI  48202
[email-masked]

The awardees will be chosen and announced at the Fall 1997 ACS  National
Meeting.

>From [email-masked] Thu Jun 26 12:00 EDT 1997
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From: Pirard Bernard B <[email-masked]>
Message-ID: <0016BC5E.MAI*/I=B/G=Bernard/S=Pirard/OU=GBJHA/PRMD=ZENECA/ADMD=PIPEX/C=GB/@MHS>
To: cclq <[email-masked]>
Subject: amber parameters and charges; summary

Dear colleagues, 
Acouple of days ago, I posted a query on AMBER parameters and charges.
Thanks to all of you who have replied. Please find enclosed a summary of
the replies. 
Sincerely
Bernard Pirard 
Computational Chemistry Group
Zeneca Agrochemicals
Jealott’s Hill
Bracknell Berkshire 
UK
[email-masked]

Bernard Pirard of Zeneca inquired about the availability of AMBER
parameters for treating generic organic molecules.  The primary
reference for the "official" AMBER force field is:

  CORNELL WD; CIEPLAK P; BAYLY CI; GOULD IR; and others.
     A SECOND GENERATION FORCE FIELD FOR THE SIMULATION OF PROTEINS, NUCLEIC
   ACIDS, AND ORGANIC MOLECULES.
     JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995 MAY 17, V117 N19:5179-5197.

The set of parameters described therein represents a complete set
for modelling proteins and nucleic acids containing standard residues.
The force field is also described as being appropriate for organic
molecules, however, the set of parameters available for modelling
such molecules is far from complete.  

When studying the interactions between small molecules and proteins
or nucleic acids, bonded parameters can often be borrowed from other 
force fields.  Charges for a new molecule, however, need to be calculated  
>from an ab initio generated HF/6-31G* wave function using the RESP protocol
as described in these references:

   BAYLY CI; CIEPLAK P; CORNELL WD; KOLLMAN PA.
     A WELL-BEHAVED ELECTROSTATIC POTENTIAL BASED METHOD USING CHARGE
   RESTRAINTS FOR DERIVING ATOMIC CHARGES - THE RESP MODEL.
     JOURNAL OF PHYSICAL CHEMISTRY, 1993 OCT 7, V97 N40:10269-10280.

   CORNELL WD; CIEPLAK P; BAYLY CI; KOLLMAN PA.
     APPLICATION OF RESP CHARGES TO CALCULATE CONFORMATIONAL ENERGIES, HYDROGEN
   BOND ENERGIES, AND FREE ENERGIES OF SOLVATION.
     JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1993 OCT 20, V115 N21:9620-9631.

Variations of the AMBER force field have been implemented in various
modelling packages and typically include the bonded and VDW parameters
but use charges derived using a simpler and less costly approach.
These implementations may be quite useful but it should be noted that
they differ from the original force field.  The "bona fide" AMBER
force field was optimized to perform well at calculating relative energies
of interaction in solution rather than, for example, screening large
sets of compounds in a DOCKing procedure. 

For those who want to carry out MD studies in solution involving
functional groups for which parameters are not available in the
JACS reference, members of the Kollman research group as well as
other members of the AMBER community often have derived such parameters.
We are currently working on developing additional parameters, however,
it will still fall to the user to calculate charges for a new molecule.

Cheers,
=Wendy Cornell
_________________________________________________________________________________
                                        
Wendy D. Cornell, Ph.D.                   
Senior Scientist
Biomolecular Structure and Drug Design Chemistry
Parke-Davis Research
Ann Arbor, MI  48105  USA

Bernard,

     If you have AMBER parameters for a particular cofactor or inhibitor,
 it may be easier to use them with Force Field Engine (FFE) in 6.3, rather than
 the original Kollman force field implementation in SYBYL. Let me know if you
 need documentation describing how to do this.

    Regards,

    Randy

We have an AMBER program suite, and the force fields are referenced
by authors. For example, the latest force field is the
Cornell et al. version. See the AMBER web page for more detailed
information, and to get the parameters. This version is optimized for liquid
simulations- be aware that some programs still use our old parameters optimized
for simulation in vacuum.

http://www.amber.ucsf.edu/amber/ff94.html

Regards
Carlos

>From [email-masked] Mon Jun 30 18:25 EDT 1997
Date: Mon, 30 Jun 1997 18:27:52 +0400
To: [email-masked]
From: Alexandre Hocquet <[email-masked]>
Subject: semantics : a summary
Content-Length: 6407
Status: R

Dear CCLers,
I have recently posted a message regarding the different possible
interpretations of the expression "molecular modelling" in the CCL
community. Thanks to all who replied.
The answers seemed to converge on the fact that two different
common interpretations may be understood (as defined in my original
 posting) and that the "classical methods"  definition originates in that
part of the "community" involved with drug design, biomolecular
modelling, etc...
Quite surprinsingly, the debate that followed focused on definitions
of "computational chemistry", a theme that has been already discussed
 (again see original message).
Anyway, be it computational chemistry or molecular modelling, it appears
that everyone has his definition, depending on what computational
chemistry (or what molecular modelling) he is involved in.
Should this situation linger on, as a proof that computational chemistry is
interdisciplinary , or do we need something like a iupac definition (as
apparently such a thing does not exist) ? Well, i guess this is another
discussion...
By the way, thanks to Georg Schrekenbach for his spelling enlightment.
Both spellings seem acceptable...
*************************************************************************
The original message  :
**************************************************************************
Dear CCLers,
While Boyd and Lipkowitz once intended to review definitions of 
"computational chemistry" (Reviews in Computational Chemistry, Vol 1, page vii),
the words "molecular modelling" still appear confusing to me :
While it seems logical to think that "molecular modelling" is that part
of "computational chemistry" that describes behaviour of molecules by
 the formalism of some theoretical model, there seems to exist in the 
community a much more restrictive use of "molecular modelling".
This second definition could be "Use of any non quantum mechanics model
 to describe the behaviour of molecules".
If one looks at the scope of the Journal of Molecular Modeling, no 
semi empirical, ab initio, dft methods are quoted, while the general 
guidelines state that "The Journal of Molecular Modeling will cover
all aspects of computational chemistry".
Another example, the ICCCRE XII congress divides the scientific program
in different topics. Amongst them :
- Semi empirical and Ab initio quantum chemistry, dft methods
- Molecular Modeling, QSAR

Any hints on a proper definition ?
Any historical reason for different uses of "molecular modelling" ?
And, above all, one or two l ?
*****************************************************************
The replies that did not appear directly in the CCL :
*****************************************************************
Alexandre ,
	In my humble opinion the term "molecular modelling" is indeed
confusing at best, i think that in most circumstances the term is used
where "molecular mechanics" would be better - i.e. solving classical
equations of motion. (and both can be abrieviated to "MM")

	noj

-- 
Dr. Noj Malcolm			
Theory Group,			
Dept. of Chemistry,		
University of Manchester,	
Oxford Road,			
Manchester.			
M13 9PL			

	Yo estoy de acuerdo con la definicion que das antes, son tecnicas 
de quimica computacional que permiten simular o medelar sistemas 
moleculares a travez de formulismo de modelos teoricos, yo pienso que no 
se restringen exclusivamente a metodos no-QM, lo que pasa es que en 
general se atribuye el termino de modelado molecular a tecnicas usadas en 
biomoleculas o en macromoleculas en general, y con tal cantidad de atomos 
quedan descartado los metodos de QM, si se quieres analizar todo esa 
macromolecula... en todo caso hay varios trabajos que mezclan tenicas de 
dinamica molecular y de QM, primero estudiando las conformaciones de la 
macromolecula con DM y luego en un entorno mas especifico, el sitio 
activo (con mucho menos atomos), con QM. La otra tecnica que creo que ha 
cobrado gran interes son los metodos hibridos QM/MM, en dosnde se definen 
zonas QM y zonas MM, se mezclan los Hamiltonianos de las zonas QM con los 
Potenciales de MM, y "ojo" que no se tienen malos resultados en cuanto a 
calculos de delta G, y otras energias. 
En resumen, el molecular modelling, a mi juicio, no esta restringido 
estrictamente a metodos no-QM, sino que a todos los metodos para 
simulacion de sistemas macromoleculares, especilemente de interes 
biologico, tal vez por la estrecha relacion que existe entre molecular 
modelling y "molecular desing", de gran interes en la industrias 
Farmaceuticas

Espero que te ayuda en algo esto, nos vemos en algun congreso!

Danilo Gonzalez.
Universidad de Santiago de Chile
Facultad de Quimica y Biologia
http://quimbio.usach.cl/~danilo/

Hi Alexandre,

this sounds like an interesting question so a summary in the CCL
would be appreciated. I have seen both of your definitions with the second
one being more often used (to increase confusion, you can also add
"simulation" vs. "modelling" ...).

One more little comment

>And, above all, one or two l ?

My dictionary (Langenscheidt English - German) doesn't contain
 "model(l)ing", however, for "model(l)er" both one and two l are offered
without any preference.

Regards, Georg

You raise an interesting point.

> Any hints on a proper definition ?

For some reason, "molecular modeling" is usually used to encompass
non-quantum-mechanical treatments of chemical structures.  In common
usage, it tends to refer to molecular mechanics as well as pure
visualization, and to things "in between", such as rule-based methods
for docking and hand-manipulation of structures, generally on a
computer.

I really don't have any good idea why or how the term got to
include these things and to exclude others, nor am I aware of
any formal definition.

Like your original comments, my sense of how the word is used
is based on how I've seen the term used -- not on any formal
definition I've seen.

	-P.

-- 
**** "Deep Blue can't triumph in the game of life." (NY Times, 5/13/97) ***
* Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 *
** NY, NY  10027;  [email-masked];  (212)854-5143;  FAX: 678-9039 ***
*MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html *

Alexandre Hocquet

Facultad de Ciencias Fisicas
Universidad de Chile
Blanco Encalada, 2008
Santiago Centro
CHILE
fono : 56 2 678 45 19
fax : 56 2 696 73 59

>From [email-masked] Mon Jun 30 18:25 EDT 1997
Date: Mon, 30 Jun 1997 18:27:55 +0400
To: [email-masked]
From: Alexandre Hocquet <[email-masked]>
Subject: French computational chemistry ?

Dear CClers, this message has been posted in French because of its local
interest. You will find a short translation into frenglish at the end.

Chers CCLeurs,
Suite aux messages de semantique sur la modelisation moleculaire et 
la "chimie computationnelle", j'aimerais faire un petit recensement
 parmi les CCLeurs de France, pour savoir qui se definit comme un 
"computational chemist".

Sauf erreur, cette expression n'existe pas en francais et la lecture
 recente des comptes rendus 1996 de situation des sections 16 et 17 
du cnrs me laisse penser qu'il existe en France : 
-des chimistes theoriciens (clairement en section 17)
-des biophysiciens (sections 20,21 ?),
mais aucune ASSOCIATION de CHIMISTES "computationnels"
(voir les definitions et la distinction avec la chimie theorique
 dans Reviews in Computational Chemistry, Vol 1, page vii)

Si vous pensez etre plus qu'un utilisateur occasionnel des techniques 
de la "chimie computationnelle", mais si vous ne vous definissez 
 ni comme un chimiste theoricien, ni comme un biophysiscien,
je serais tres heureux de recevoir votre reponse .

Je ferais un resume si il y a suffisament d'interet.
*********************************************************************
Due to the fact that "computationnal chemistry" does not exist in the 
french language as it seems that no "computational chemist" 
community has been formed in France, i intend to make a census of 
whoever considers himself as a computational chemist and works in
 France. If you're not french but want to comment on this, you are
 welcome.
***********************************************************************
Alexandre Hocquet

Facultad de Ciencias Fisicas
Universidad de Chile
Blanco Encalada, 2008
Santiago Centro
CHILE
fono : 56 2 678 45 19
fax : 56 2 696 73 59

>From [email-masked] Mon Jun 30 10:42 EDT 1997
Date: Mon, 30 Jun 1997 16:41:19 +0200 (W. Europe Daylight Time)
From: "Lestaw K. Bieniasz" <[email-masked]>
To: [email-masked]
Subject: Re: CCL:CC semantics
Content-Length: 3365
Status: RO

				Tuebingen, 27.06.97

Dear Dr. Buyong Ma,

Yes, you're right I posted that letter a couple of months ago,
but there were not too many responses.
(Nevertheless, I wish to thank to those who responded).

My personal point of view (unfortunately not shared with the
scientific establishment) is that we should not pay
too much attention to the classification of scientific activities.
It should not really matter whether somebody is doing chemistry or physics
or physical chemistry, etc. The only thing that matters should be the
quality of the research. I wish we all could say "we do science",
instead of trying hard to specify which particular part of it we do.
I am sure this attitude would bring more progress into science, since
it would allow the individuals to freely cross the real or imaginary
borders between various research areas. This way of looking at science
would also remove some of the semantic difficulties that you mention.

But of course this is an idealistic dream, since in reality
everything in science is divided into disciplines, and this system is very
conservative, although as you rightly point out, there is a lot of
overlapping between the disciplines (often viewed as uncomfortable).
Now, since it looks that we indeed have to live in this reality, then
my suggestion simply is that we use right words to denote things.
Thus, in my opinion the term "computational chemistry" should be used to
denote what it (literally) means. And it certainly means a combination
of chemistry and computations, without specifying whether the subject is
molecular or not.  This understanding of computational chemistry is in a
certain contrast to the current practice, in which the term "computational
chemistry" is often interpreted in a much narrower sense, so that if my
suggestion is accepted, it would indeed mean a certain enlargement of the
scope of the (currently understood) computational chemistry.
Note, however, that I have not invented this "new" definition, because
it is already contained in one of the volumes of "Reviews in Computational
Chemistry" !

In the same spirit, I think that the term "molecular modelling" should
be used to denote any kind of modelling in which the assumed molecular
structure of matter plays a central role, independently of whether the
modelling is computational or not, although in practice it will of course
be mostly computational, because non-computational methods are of limited
use here.

With best regards,

			Yours sincerely,

						L.Bieniasz

*-------------------------------------------------------------------*
|                        Dr. Leslaw Bieniasz                        |
| temporary address: (3rd April 1997 - 31st August 1997)            |
|       Institut fuer Organische Chemie, Universitaet Tuebingen     |
|          Auf der Morgenstelle 18, 72076 Tuebingen, Germany.       |
|              E-mail: [email-masked]           |
*-------------------------------------------------------------------*
| permanent address:                                                |
| Institute of Physical Chemistry of the Polish Academy of Sciences,| 
| Molten Salts Laboratory, ul. Zagrody 13, 30-318 Cracow, Poland.   | 
|                   E-mail:  [email-masked]                 |
*-------------------------------------------------------------------*