From owner-chemistry@ccl.net Mon May  9 02:16:00 2011
From: "Andrew Dalke dalke/a\dalkescientific.com" <owner-chemistry ~ server.ccl.net>
To: CCL
Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN?
Message-Id: <-44593-110509021248-26739-u4+fHzOCz0Y1+GXNA4dF2A ~ server.ccl.net>
X-Original-From: Andrew Dalke <dalke|dalkescientific.com>
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Date: Mon, 9 May 2011 08:12:35 +0200
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Sent to CCL by: Andrew Dalke [dalke . dalkescientific.com]
On May 8, 2011, at 8:41 AM, Frank Neese neese-,-thch.uni-bonn.de wrote:
> Maybe a few words from a developper of a large code: 
> 
> when i started the ORCA program in the late 90s we decided to use C++
> because i felt that it would be much easier to keep the code well
> structured and organized in manageable pieces. 

I don't develop quantum chemistry software but I have done classical
MD and I want to reinforce Frank's statement.

In the mid-1990s I was one of the original developers of NAMD, a
high-performance/large-scale MD program designed for distributed
computing.

We chose C++ in part because we believed that the hard part of the
program was the managing the data structures for spatial
decomposition and interprocess communications. Quoting from
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2486339/
(none of the original NAMD authors are on that paper so this
isn't a reflection of our biases)

   While this presents a serious impediment to other programs, 
   NAMD’s message-driven architecture is able to automatically
   interleave the latency-sensitive FFT algorithm with the
   dominant and latency-tolerant short-range nonbonded calculation

I don't mean to say that Fortran or any other system couldn't
do the same thing. I bring this up to highlight that the code
*architecture* is the dominant cost and consideration, and the
ability to do fast numeric calculations on matrices, while important,
is not the main consideration even in a task which is traditionally
considered one of Fortran's fortes.

> The rest is more or less a matter of organizational convenience. Present day multicore machines also appear to be rather limited by  memory bandwidth than by floating point performance. 

I'll add to this statement. I am amazed that one memory fetch takes so long.

This influential paper from 2007 ("What Every Programmer Should Know About Memory")
  http://www.akkadia.org/drepper/cpumemory.pdf

points out on p.16 that a fetch from main memory is about 240 clock cycles.
It's likely that doing 60 instructions in order to not pull something from
cache is faster.

This is quite different from the computers I started off with.

I've also had to learn how cache lines affect performance.

> Concerning the whole argument with 1-based arrays - i don't get that. What is the virtue of having arrays start at 1 other than 
> that some people got used to it. After a short while one is just used to zero based arrays and there is no problem. 

Agreed!


				Andrew
				dalke]![dalkescientific.com


From owner-chemistry@ccl.net Mon May  9 04:22:00 2011
From: "Praveen Kumar Shrivastava praveenshrivastav(~)gmail.com" <owner-chemistry(-)server.ccl.net>
To: CCL
Subject: CCL: chemoinformatics
Message-Id: <-44594-110509040324-4854-PtGqq847BwM8mvu7ADtchQ(-)server.ccl.net>
X-Original-From: Praveen Kumar Shrivastava <praveenshrivastav]_[gmail.com>
Content-Type: multipart/alternative; boundary=90e6ba6e85525c140704a2d3458f
Date: Mon, 9 May 2011 13:33:12 +0530
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Sent to CCL by: Praveen Kumar Shrivastava [praveenshrivastav]|[gmail.com]
--90e6ba6e85525c140704a2d3458f
Content-Type: text/plain; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Dr Rodolfo G=F3mez

I wish to include following concept in curriculum.

   - Graph Theory
   - Biology
   - Molecular Biology
   - Fundamental of Computer Science.


   - Programing language C++ and JAVA

I hope you will agree with my wish list for Undergraduate cource.

With my best rgards

Praveen Kumar Shrivastava
On Sun, May 8, 2011 at 11:02 AM, Rodolfo Gomez rgbccl/./gmail.com <
owner-chemistry{:}ccl.net> wrote:

> Dear CCLrs,
>
> Recently my faculty is considering to offer an undergraduate course on
> Chemoinformatics, for chemistry students. Though I=B4ve been working a bi=
t on
> computational chemistry, I do not feel I have the proper vision to built =
up
> a syllabus proposal, or even for giving a reasonable criticism of anyone
> else proposal.
>
> I would really appreciate your opinion on what should be included in a
> course of such a level?
>
> Thanks in advance for your kind reply.
>
> Rodolfo G=F3mez
>

--90e6ba6e85525c140704a2d3458f
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

<br><br><div class=3D"gmail_quote">Dear Dr Rodolfo G=F3mez</div><div class=
=3D"gmail_quote"><br></div><div class=3D"gmail_quote">I wish to include fol=
lowing concept in curriculum.</div><div class=3D"gmail_quote"><div><ul><li>=
Graph Theory</li>
<li>Biology</li><li>Molecular Biology</li><li>Fundamental of Computer Scien=
ce.</li></ul></div></div><div><ul><li>Programing language C++ and JAVA</li>=
</ul></div><div>I hope you will agree with my wish list for Undergraduate c=
ource.</div>
<div><br></div><div>With my best rgards</div><div><br></div><div>Praveen Ku=
mar Shrivastava=A0</div><div class=3D"gmail_quote">On Sun, May 8, 2011 at 1=
1:02 AM, Rodolfo Gomez rgbccl/./<a href=3D"http://gmail.com">gmail.com</a> =
<span dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry{:}ccl.net">owner-chem=
istry{:}ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex;"><div>Dear CCLrs,</div>
<div>=A0</div>
<div>Recently my faculty is considering to offer an undergraduate course on=
 Chemoinformatics, for chemistry students. Though I=B4ve been working a bit=
 on computational chemistry, I do not feel I have the proper vision=A0to bu=
ilt up a syllabus proposal, or even=A0for giving a reasonable=A0criticism o=
f anyone else proposal. </div>


<div>=A0</div>
<div>I would really appreciate your opinion on what=A0should be included in=
 a course of such a level?</div>
<div>=A0</div>
<div>Thanks in advance for your kind reply.</div>
<div>=A0</div>
<div>Rodolfo G=F3mez</div>
</blockquote></div><br>

--90e6ba6e85525c140704a2d3458f--


From owner-chemistry@ccl.net Mon May  9 04:57:00 2011
From: "uekstrom-$-gmail.com uekstrom-$-gmail.com" <owner-chemistry[]server.ccl.net>
To: CCL
Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN?
Message-Id: <-44595-110509043759-16566-8OAaa+dQT0difPikYxssVg[]server.ccl.net>
X-Original-From: "uekstrom-x-gmail.com" <uekstrom-x-gmail.com>
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Date: Mon, 9 May 2011 10:37:51 +0200
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Sent to CCL by: "uekstrom,gmail.com" [uekstrom,gmail.com]
>> The rest is more or less a matter of organizational convenience. Present day multicore machines also appear to be rather limited by  memory bandwidth than by floating point performance.
>
> I'll add to this statement. I am amazed that one memory fetch takes so long.

Indeed! In the Dirac program we have matrices of quaternions. These
can be packed either as A(N,N,4) or A(4,N,N). For historical reasons
the A(N,N,4) packing was chosen in the nineties. Now, because memory
is slow it turns out that this packing is _four times_ slower than the
alternative for multiplication of quaternion matrices. However,
changing the program at this point would be way too much work, so we
constantly run with a performance penalty of 4 in many parts of the
code. If the program was written in a more object oriented way, with
abstract matrices, it would be trivial to change the packing and
achieve an instant speedup. I think the choice between abstraction and
performance is a false one -- the abstract code wins out in the long
run.

Ulf


From owner-chemistry@ccl.net Mon May  9 07:27:00 2011
From: "Michel Petitjean petitjean.chiral]*[gmail.com" <owner-chemistry^^server.ccl.net>
To: CCL
Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN?
Message-Id: <-44596-110509071104-27220-bTXbk1GmsQF8sskol5MgtA^^server.ccl.net>
X-Original-From: Michel Petitjean <petitjean.chiral^gmail.com>
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Date: Mon, 9 May 2011 13:10:54 +0200
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Sent to CCL by: Michel Petitjean [petitjean.chiral|-|gmail.com]
Dear Ulf,

If you really got tridimensional arrays from calling routines, you can
declare them as A(N*N*4) or A(*) in your own routines.
Did you try that and does it save execution time ?
Regarding the change of format N,N,4 vs. 4,N,N: each time that you
decide about a format, you must decide to access to your structure via
a specific set routines, and ONLY through these routines. Just as for
classes, if some change occurs, you only need to change the pack of
dedicated routines.
Further refinement may include a parameter which specify which kind of
format is to be used, etc.
All the benefits of OO programming, classes, etc., can be retrieved.
This kind of exercise is common is some companies which maintain large
programmes libraries.
You can get garbage with any programming language, including C++,
java, ADA, etc.
It is not a matter of language: it is a matter of project management.

Best,
Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral(a)gmail.com (preferred),
michel.petitjean(a)univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html


2011/5/9 uekstrom-$-gmail.com uekstrom-$-gmail.com <owner-chemistry(a)ccl.net>:
>
> Sent to CCL by: "uekstrom,gmail.com" [uekstrom,gmail.com]
>>> The rest is more or less a matter of organizational convenience. Present day multicore machines also appear to be rather limited by  memory bandwidth than by floating point performance.
>>
>> I'll add to this statement. I am amazed that one memory fetch takes so long.
>
> Indeed! In the Dirac program we have matrices of quaternions. These
> can be packed either as A(N,N,4) or A(4,N,N). For historical reasons
> the A(N,N,4) packing was chosen in the nineties. Now, because memory
> is slow it turns out that this packing is _four times_ slower than the
> alternative for multiplication of quaternion matrices. However,
> changing the program at this point would be way too much work, so we
> constantly run with a performance penalty of 4 in many parts of the
> code. If the program was written in a more object oriented way, with
> abstract matrices, it would be trivial to change the packing and
> achieve an instant speedup. I think the choice between abstraction and
> performance is a false one -- the abstract code wins out in the long
> run.
>
> Ulf
>


From owner-chemistry@ccl.net Mon May  9 08:03:00 2011
From: "karthikeyan m.karthikeyan%x%ncl.res.in" <owner-chemistry * server.ccl.net>
To: CCL
Subject: CCL:G: chemoinformatics
Message-Id: <-44597-110509060438-8221-qFAeJuu0oV0CroGtBJXKvQ * server.ccl.net>
X-Original-From: karthikeyan <m.karthikeyan%a%ncl.res.in>
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Date: Mon, 9 May 2011 15:33:48 +0530
MIME-Version: 1.0


Sent to CCL by: karthikeyan [m.karthikeyan~~ncl.res.in]
--------------050603000903060403010505
Content-Type: text/plain; charset="iso-8859-1"; format=flowed
Content-Transfer-Encoding: quoted-printable


Sometime back when I was asked suggest the syllabus for BSc Chemoinformatic=
s in India, LDC-Madurai
I proposed the following: (May be it can be extended depending on the level=
 of depth and
interest of both student/teachers). This subject should be combined with ot=
her basic
courses on computers & basic chemistry (introduction to organic, inorganic,=
 analytical, physical, environmental
biochemistry etc.,) I am interested to know more about BSc Level chemoinfor=
matics syllabus.
Please keep me updated.

Source Document (PDF): URL:

  http://tinyurl.com/5w4cl5b

M.Karthikeyan
Scientist, NCL-Pune
http://moltable.ncl.res.in/


CHE5421M - CHEMINFORMATICS
SEMESTER V
          THEORY                 4 hrs / week
UNIT I: ELEMENTS OF CHEMINFORMATICS
History of chemoinformatics, Definition of Chemoinformatics, Chemical Struc=
ture representation. Introduction to chemical structure file formats. Linea=
r, 2D and 3D representations. Connection Tables, Molecular structure Search=
ing techniques. Introduction to Molecular Fingerprints. Similarity metrics =
(Tanimoto Coefficient, Eucledien distance).  Computer representation of mol=
ecules- Chemical databases -data search -2D and 3D searching. Interconversi=
on of 2D to 3D optimization techniques             10 hrs
UNIT II: COMBINATORIAL CHEMISTRY
Combinatorial chemistry - Molecular Scaffolds, Design of Scaffolds from lib=
rary of molecules. Focused virtual library design and analysis. principles =
and methods. Rule of five, Druglikeliness, Leadlikeliness, Screening, Drug =
design and combinatorial libraries- case studies.                       25h=
rs
UNIT III : DRUG DESIGN AND DISCOVERY
Contour of Drugs --Development of New Drugs - molecular recognition in drug=
 design- Introduction to molecular diversity ; molecular similarity (Tanimo=
to, Eucledian, Dice, Cosine) - molecular descriptors (1D, 2D, 3D)- partitio=
n coefficient (LogP)- molar refractivity-pharmacophore keys- similarity cal=
culation stereochemistry in drug design -Prodrugs and Soft Drugs -Drug Targ=
ets -Drug Solubility - Lead optimization Molecular Diversity- natural Resou=
rces of lead Compounds -case studies.             25 hrs
UNIT IV : DATABASES
Chemical database design- Chemical Abstract Service, Pubchem (Compounds, Su=
bstances, Bioassay), PubMed, EPA, FDA, RTECTS, NIOSTIC, DrugBank, ChemBank,=
 ChemSpider, ChemExper, SPECS, Commercial Chemical Suppliers Database, NCI,=
 MOLTABLE.                              35 hrs

REFERENCE BOOKS:
1.    Larsen et al (ed), Textbook of drug design and discovery, 3rd edition=
, Taylor and Francis, London and New York, 2004.
2.    Ashutosh Kar, Medicinal Chemistry, III ed, New Age International publ=
ishers, New Delhi.
CHE 6524M - COMPUTATIONAL CHEMISTRY AND MOLECULAR MODELING

SEMESTER VI
LAB CUM THEORY             5 hrs/week
UNIT I: COMPUTATIONAL CHEMISTRY
Experimental aspects and computer models of molecules and their behavior in=
 gas and condensed phases; quantum and molecular mechanics - Force field an=
d its applications- multiple regression analysis- implicit and explicit sol=
vation models; conformational analysis; energy minimisation; Basic concepts=
 of  Ab Initio molecular dynamics and Monte Carlo simulations.             =
            (Theory: 20 hrs; Lab: 15 hrs)
Labwork with software like Gaussian, MOPAC, MOE, JCHEM, MarvinSketch, Marvi=
nView, MarvinSpace

UNIT II: MOLECULAR MODELING
Ligand based Drug Design, Quantitative structure-activity relationships (QS=
AR)- Introduction of Molecular Descriptors (1D,2D and 3D), Statistical anal=
ysis- Linear and Non linear Methods, PLS, PCA, PCR, ANN, kNN, SVM, Binary m=
ethods. Elementary ideas of comparative molecular field analysis (CoMFA). P=
harmacophore modeling, structure-based design; docking and scoring function=
s; Structure based de novo design techniques -Molecular Docking, Active Sit=
e characterization, Case study of designing HIV I protease Inhibitor-  Quan=
titative structure-property relationships (QSPR) - Predicting Melting Point=
, Solubility, Boiling point, TPSA etc.,. Quantitative Structure Toxicity Re=
lationships (QSTR), Aquatic Toxicity, Carcinogenicity, Mutagenicity,       =
                                           (Theory: 30 hrs; Lab: 30 hrs)

Chemical Databases
Introduction to publicly available molecular databases, Pubchem, Literature=
 databases (PubMed), Introduction to NCBI web resource. Learning MeSH, NLM =
Database, NCI Database, DRUGBank, FDA Drugs, EPA Chemical Databases, RTECS =
etc., Searching and Retrieving molecular data and other physico chemical, b=
iological, toxicological data from web sources for QSAR, QSPR and QSTR rela=
ted studies. (Theory: 20 hrs; Lab: 20 hrs)


REFERENCE BOOK:
1.    Leach A.R, Molecular Modelling: Principles and applications, 2nd edit=
ion, Prentice Hall, 2001.
2.    TextBook of Chemoinformatics, Gasteiger
3.    Handbook of chemoinformatics, Gasteiger
4.    Introduction to Chemoinformatics, Leach




About

On 5/9/2011 1:33 PM, Praveen Kumar Shrivastava praveenshrivastav(~)gmail.co=
m wrote:


Dear Dr Rodolfo G=F3mez

I wish to include following concept in curriculum.

 *   Graph Theory
 *   Biology
 *   Molecular Biology
 *   Fundamental of Computer Science.

 *   Programing language C++ and JAVA

I hope you will agree with my wish list for Undergraduate cource.

With my best rgards

Praveen Kumar Shrivastava
On Sun, May 8, 2011 at 11:02 AM, Rodolfo Gomez rgbccl/./gmail.com<http://gm=
ail.com> <owner-chemistry]-[ccl.net<mailto:owner-chemistry]-[ccl.net>> wrot=
e:
Dear CCLrs,

Recently my faculty is considering to offer an undergraduate course on Chem=
oinformatics, for chemistry students. Though I=B4ve been working a bit on c=
omputational chemistry, I do not feel I have the proper vision to built up =
a syllabus proposal, or even for giving a reasonable criticism of anyone el=
se proposal.

I would really appreciate your opinion on what should be included in a cour=
se of such a level?

Thanks in advance for your kind reply.

Rodolfo G=F3mez




________________________________
Disclaimer:

This message and the information contained herein is proprietary and confid=
ential and subject to the policy statement of the National Chemical Laborat=
ory, Pune, India. You may review the policy at http://www.ncl-india.org/com=
mon/webmailDisclaimer.htm

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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta http-equiv=3D"Content-Type" content=3D"text/html; charset=3Diso-8859-=
1">
<title></title>
</head>
<body bgcolor=3D"#ffffff" text=3D"#000000">
<br>
Sometime back when I was asked suggest the syllabus for BSc Chemoinformatic=
s in India, LDC-Madurai<br>
I proposed the following: (May be it can be extended depending on the level=
 of depth and<br>
interest of both student/teachers). This subject should be combined with ot=
her basic<br>
courses on computers &amp; basic chemistry (introduction to organic, inorga=
nic, analytical, physical, environmental<br>
biochemistry etc.,) I am interested to know more about BSc Level chemoinfor=
matics syllabus.<br>
Please keep me updated.<br>
<br>
Source Document (PDF): URL: <br>
<br>
&nbsp; <b><a class=3D"moz-txt-link-freetext" href=3D"http://tinyurl.com/5w4=
cl5b">http://tinyurl.com/5w4cl5b</a></b><br>
<br>
M.Karthikeyan<br>
Scientist, NCL-Pune<br>
<a class=3D"moz-txt-link-freetext" href=3D"http://moltable.ncl.res.in/">htt=
p://moltable.ncl.res.in/</a><br>
<br>
<br>
CHE5421M - CHEMINFORMATICS<br>
SEMESTER V<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; THEORY &nbsp;&nbsp;&=
nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; 4 hrs / week=
<br>
UNIT I: ELEMENTS OF CHEMINFORMATICS<br>
History of chemoinformatics, Definition of Chemoinformatics, Chemical Struc=
ture representation. Introduction to chemical structure file formats. Linea=
r, 2D and 3D representations. Connection Tables, Molecular structure Search=
ing techniques. Introduction to
 Molecular Fingerprints. Similarity metrics (Tanimoto Coefficient, Eucledie=
n distance).&nbsp; Computer representation of molecules- Chemical databases=
 -data search &#8211;2D and 3D searching. Interconversion of 2D to 3D optim=
ization techniques &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;=
 10 hrs<br>
UNIT II: COMBINATORIAL CHEMISTRY&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp=
;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
Combinatorial chemistry &#8211; Molecular Scaffolds, Design of Scaffolds fr=
om library of molecules. Focused virtual library design and analysis. princ=
iples and methods. Rule of five, Druglikeliness, Leadlikeliness, Screening,=
 Drug design and combinatorial libraries&#8211;
 case studies.&nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbs=
p;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; 25hrs<br>
UNIT III : DRUG DESIGN AND DISCOVERY &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; =
&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;=
 <br>
Contour of Drugs &#8211;-Development of New Drugs &#8211; molecular recogni=
tion in drug design- Introduction to molecular diversity ; molecular simila=
rity (Tanimoto, Eucledian, Dice, Cosine) &#8211; molecular descriptors (1D,=
 2D, 3D)- partition coefficient (LogP)&#8211; molar refractivity-pharmacoph=
ore
 keys- similarity calculation stereochemistry in drug design -Prodrugs and =
Soft Drugs -Drug Targets -Drug Solubility &#8211; Lead optimization Molecul=
ar Diversity- natural Resources of lead Compounds &#8211;case studies. &nbs=
p;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; 25 hrs<br>
UNIT IV : DATABASES<br>
Chemical database design- Chemical Abstract Service, Pubchem (Compounds, Su=
bstances, Bioassay), PubMed, EPA, FDA, RTECTS, NIOSTIC, DrugBank, ChemBank,=
 ChemSpider, ChemExper, SPECS, Commercial Chemical Suppliers Database, NCI,=
 MOLTABLE.&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &=
nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp;
 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; 35 hrs<br>
<br>
REFERENCE BOOKS: <br>
1.&nbsp;&nbsp;&nbsp; Larsen et al (ed), Textbook of drug design and discove=
ry, 3rd edition, Taylor and Francis, London and New York, 2004.<br>
2.&nbsp;&nbsp;&nbsp; Ashutosh Kar, Medicinal Chemistry, III ed, New Age Int=
ernational publishers, New Delhi.<br>
CHE 6524M - COMPUTATIONAL CHEMISTRY AND MOLECULAR MODELING<br>
<br>
SEMESTER VI<br>
LAB CUM THEORY&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbs=
p;5 hrs/week&nbsp;&nbsp; <br>
UNIT I: COMPUTATIONAL CHEMISTRY&nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;=
&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
Experimental aspects and computer models of molecules and their behavior in=
 gas and condensed phases; quantum and molecular mechanics - Force field an=
d its applications- multiple regression analysis- implicit and explicit sol=
vation models; conformational analysis;
 energy minimisation; Basic concepts of&nbsp; Ab Initio molecular dynamics =
and Monte Carlo simulations. &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&n=
bsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; (Theory=
: 20 hrs; Lab: 15 hrs)<br>
Labwork with software like Gaussian, MOPAC, MOE, JCHEM, MarvinSketch, Marvi=
nView, MarvinSpace<br>
<br>
UNIT II: MOLECULAR MODELING&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nb=
sp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; &nbsp;&nbsp;&nbsp; <br>
Ligand based Drug Design, Quantitative structure-activity relationships (QS=
AR)- Introduction of Molecular Descriptors (1D,2D and 3D), Statistical anal=
ysis- Linear and Non linear Methods, PLS, PCA, PCR, ANN, kNN, SVM, Binary m=
ethods. Elementary ideas of comparative
 molecular field analysis (CoMFA). Pharmacophore modeling, structure-based =
design; docking and scoring functions; Structure based de novo design techn=
iques &#8211;Molecular Docking, Active Site characterization, Case study of=
 designing HIV I protease Inhibitor-&nbsp;
 Quantitative structure-property relationships (QSPR) &#8211; Predicting Me=
lting Point, Solubility, Boiling point, TPSA etc.,. Quantitative Structure =
Toxicity Relationships (QSTR), Aquatic Toxicity, Carcinogenicity, Mutagenic=
ity, &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;&nbsp; &nbsp;(Theory: 30=
 hrs; Lab: 30 hrs)<br>
<br>
Chemical Databases<br>
Introduction to publicly available molecular databases, Pubchem, Literature=
 databases (PubMed), Introduction to NCBI web resource. Learning MeSH, NLM =
Database, NCI Database, DRUGBank, FDA Drugs, EPA Chemical Databases, RTECS =
etc., Searching and Retrieving molecular
 data and other physico chemical, biological, toxicological data from web s=
ources for QSAR, QSPR and QSTR related studies. (Theory: 20 hrs; Lab: 20 hr=
s)<br>
<br>
<br>
REFERENCE BOOK: <br>
1.&nbsp;&nbsp;&nbsp; Leach A.R, Molecular Modelling: Principles and applica=
tions, 2nd edition, Prentice Hall, 2001.<br>
2.&nbsp;&nbsp;&nbsp; TextBook of Chemoinformatics, Gasteiger<br>
3.&nbsp;&nbsp;&nbsp; Handbook of chemoinformatics, Gasteiger<br>
4.&nbsp;&nbsp;&nbsp; Introduction to Chemoinformatics, Leach<br>
<br>
<br>
<br>
<br>
About <br>
<br>
On 5/9/2011 1:33 PM, Praveen Kumar Shrivastava praveenshrivastav(~)gmail.co=
m wrote:
<blockquote cite=3D"mid:-id%234bi-44594-110509040324-4854-Y8WHN%2F81gFPd8rE=
tlt5FkA^server.ccl.net" type=3D"cite">
<br>
<br>
<div class=3D"gmail_quote">Dear Dr Rodolfo G=F3mez</div>
<div class=3D"gmail_quote"><br>
</div>
<div class=3D"gmail_quote">I wish to include following concept in curriculu=
m.</div>
<div class=3D"gmail_quote">
<div>
<ul>
<li>Graph Theory </li><li>Biology </li><li>Molecular Biology </li><li>Funda=
mental of Computer Science. </li></ul>
</div>
</div>
<div>
<ul>
<li>Programing language C&#43;&#43; and JAVA </li></ul>
</div>
<div>I hope you will agree with my wish list for Undergraduate cource.</div=
>
<div><br>
</div>
<div>With my best rgards</div>
<div><br>
</div>
<div>Praveen Kumar Shrivastava&nbsp;</div>
<div class=3D"gmail_quote">On Sun, May 8, 2011 at 11:02 AM, Rodolfo Gomez r=
gbccl/./<a moz-do-not-send=3D"true" href=3D"http://gmail.com">gmail.com</a>
<span dir=3D"ltr">&lt;<a moz-do-not-send=3D"true" href=3D"mailto:owner-chem=
istry]-[ccl.net">owner-chemistry]-[ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin: 0pt 0pt 0pt
          0.8ex; border-left: 1px solid rgb(204, 204, 204);
          padding-left: 1ex;">
<div>Dear CCLrs,</div>
<div>&nbsp;</div>
<div>Recently my faculty is considering to offer an undergraduate course on=
 Chemoinformatics, for chemistry students. Though I=B4ve been working a bit=
 on computational chemistry, I do not feel I have the proper vision&nbsp;to=
 built up a syllabus proposal, or even&nbsp;for
 giving a reasonable&nbsp;criticism of anyone else proposal. </div>
<div>&nbsp;</div>
<div>I would really appreciate your opinion on what&nbsp;should be included=
 in a course of such a level?</div>
<div>&nbsp;</div>
<div>Thanks in advance for your kind reply.</div>
<div>&nbsp;</div>
<div>Rodolfo G=F3mez</div>
</blockquote>
</div>
<br>
</blockquote>
<br>
<br>
<br>
<hr>
<font face=3D"Verdana" color=3D"Green" size=3D"1">Disclaimer:<br>
<br>
This message and the information contained herein is proprietary and confid=
ential and subject to the policy statement of the National Chemical Laborat=
ory, Pune, India. You may review the policy at http://www.ncl-india.org/com=
mon/webmailDisclaimer.htm<br>
</font>
</body>
</html>

--------------050603000903060403010505--


From owner-chemistry@ccl.net Mon May  9 08:37:00 2011
From: "Vincent Leroux vincent.leroux---loria.fr" <owner-chemistry.@.server.ccl.net>
To: CCL
Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN?
Message-Id: <-44598-110509070109-16664-Czqsf6f/SsQTULyy08p/Mg.@.server.ccl.net>
X-Original-From: Vincent Leroux <vincent.leroux,,loria.fr>
Content-Transfer-Encoding: 8bit
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Date: Mon, 09 May 2011 13:00:55 +0200
MIME-Version: 1.0


Sent to CCL by: Vincent Leroux [vincent.leroux-*-loria.fr]
Hello all,

I am quite a rare specimen as I am on my 30s and I did mostly learn 
Fortran during my master studies, in scientific programming-oriented 
courses. That was 10 years ago, and at the time Fortran teaching was 
already considered as an heresy. Retrospectively, I think I was really 
lucky, because I think that gave me a pragmatic approach to the coding 
practice...

I agree that Fortran, while it is not dead yet, is unfortunately 
declining constantly, as most master students were never introduced to 
it during their studies. Why is that so? What I witnessed personally is 
that too often, the strongest advocates of Fortran as a core scientific 
programming language are not teaching it. Do any of you know many 
computational chemists that directly teach scientific programming at 
universities? Now, in Europe, many students do not even come to learn C. 
For the majority of computer science specialists that are in charge of 
the teaching, Fortran is simply obsolete, and high-level programming 
with Java, Python or Ruby is without any doubt more useful than 
low-level C/C++...

During my research career, I had to program in both C and Fortran, but I 
never got involved in very large projects (so I was exposed to few C++ 
that tend to dominate those). I confirm something that was already 
mentioned in the discussion: most Fortran code I found was written in a 
very conservative F77 style, and in a minority of cases, really painful 
spaghetti-F66. In all cases, independently of the language, the major 
problem was the lack of documentation. I do think maintaining large 
Fortran projects may turn into a nightmare easily and I perfectly 
understand why C++ is often being preferred, as it provides a better way 
to abstract complex structures and relations. As for molecular 
mechanics, one can compare the degree of clarity of CHARMM code 
(Fortran) compared to NAMD (C++), this is quite shocking...

However, writing very clean Fortran 77 code is definitely possible: 
TINKER is one good example. It looks like an exception, unfortunately.



As for *teaching* scientific programming, I am a strong advocate of 
Fortran 77, for several reasons:

- The official F77 specifications are very concise, less than 100 pages. 
Students can actually read them, and have a complete grasp over the 
language. Is that possible with C, C++, Java, Python?

- What is "missing" in Fortran 77 (mostly direct memory access, 
recursivity, definition of complex data structures) are indeed basic 
features of any modern programming language, but those features should 
never be "overused". I think it is good that students first understand 
how it is possible to live without those in many cases, so that they do 
not grow bad habits like systematically using more pointers and OOP 
concepts than necessary...

- Provided GOTO, IMPLICIT and EQUIVALENCE are not used in evil ways, 
reducing the number of lines of code in a Fortran 77 routine almost 
always results in more elegant and cleaner code. The same goes for 
Python. With C/C++, reducing code size too often means using "dirty 
tricks" that only obfuscate things: it is always possible to go too far. 
Learning to code cleanly is crucial, and I consider Fortran 77 perfectly 
suited for that

- The good old g77 compiler, freely available on all platforms (even 
Windows...) accepts F90-style coding so that no one needs to be bound to 
the punch card remains of the dinosaur age. Loop labels and control 
statements like cycle/exit are there and really clarify things when 
correctly used, as they avoid GOTO overdose

- It might be surprising to any programmer not used to Fortran, but this 
language, while it was never meant for that, is very capable for most 
tasks outside pure numerical calculations, including, as Michel 
mentioned, processing text strings. Of course, this is not Perl or Awk, 
but Fortran 77 is way better than C/C++ in that regard

- This is not very important, but I have to mention that. No student 
understands why the hell indexes should start at zero. I can only agree. 
This is just plain annoying, even after getting used to this, and 
knowing it can (and should) be hidden behind another layer of 
abstraction in C/C++ code with external libraries I am still annoyed, 
because I started with Fortran and I *know* this should *not* be like 
this  ;-)

- AFAIK, there is no programming language that is simple (meaning: 
complete specifications < 1000 pages), promotes simplicity and is 
powerful (both numerically and functionally). I think that to teach, the 
best is to choose a non-exotic language that is simple and promotes 
simplicity, even if it misses some features of modern programming 
languages. Python is powerful and explicitly promotes simplicity (so if 
only a single language is to be chosen for teaching, it is not a bad 
choice), but is not simple. Ruby looks quite similar in that regard, but 
Python has better libraries for computational chemistry. C is simple and 
powerful, but certainly does not promote simplicity. C++ and Fortran 90+ 
are very powerful but I think they are quite hard for beginners. 
Teachers should also definitely do the students a favor by not 
advocating the stability-by-verbosity philosophy of Java or Ada, that 
only makes them hate programming... Fortran 77, Awk and Lisp are, in my 
opinion, the only languages to choose from... a combination of F77 and 
Awk may be perfect for teaching the basics, in a computational chemistry 
perspective: numerical calculations with the former, text processing 
(and some basic Unix shell usage) with the latter... IMHO, Python, C/C++ 
and OOP concepts should be introduced at a more advanced level.



Regarding the current teaching of scientific programming, I also have to 
say that I agree with Michel, as probably most users of the mailing 
list: computational chemistry with Windows, this is simply not serious. 
I think advocating the use of Unix is way more important than debating 
over C++/Fortran. When a theoretical chemistry-specialized masters 
student happens to never have used a Unix terminal in his/her life (this 
is not uncommon these days), his/her knowledge of C or Fortran should be 
the least of the worries for teachers and supervisors... A related 
problem is that Windows is a de facto standard for many people, this may 
include regulators in private companies and universities. How could we 
expect better programming practices in the computer chemistry field (and 
I would consider better Fortran knowledge as a clear improvement) if 
students/employees are forced into using Windows/Visual Studio? From 
time to time, some Chinese/Indian master/PhD students will ask how to do 
something under Windows on this mailing list, they may not have the 
choice...

Eventually, for large projects, Python may be used as a wrapper for a 
mix of (possibly heterogeneous) C, C++ and Fortran routines. Today, 
Python seems to be a good alternative to the "C++ or Fortran" dilemna... 
It is possible to use C/C++ when it is better suited than Fortran, use 
Fortran when it is better than C/C++, keep the best of both worlds, 
restricting C/C++/Fortran low-level coding to the minimum (that should 
then be easier to isolate performance bottlenecks...), with an elegant 
and very powerful high-level language on top. There are projects in the 
computational chemistry area using such a Python-wrapping approach 
(FLIPDock comes to my mind), but I do not know how many exactly. I think 
it would be interesting if there was some people here to share expertise 
in such a coding strategy for medium/large projects.

Regards,
VL



Le 07/05/11 04:33, Jun Zhang coolrainbow()yahoo.cn a écrit :
>
> Sent to CCL by: Jun Zhang [coolrainbow]*[yahoo.cn]
> Hello Everyone:
>
> Many new developed quantum chemistry software have been written in C++ rather than FORTRAN. Although the compilers for C++ are developing, however, due to C++'s inherent complexity, I don't think it is easier to optimize a C++ code than FORTRAN code for compilers. So why so many have chosen C++? Is it due to developing efficiency? Any suggestions will be appreciated.
>
> Jun Zhang
> Nankai University
> coolrainbow- -yahoo.cn
>
>


From owner-chemistry@ccl.net Mon May  9 09:12:00 2011
From: "Tasaka Tomo t.tasaka###gmail.com" <owner-chemistry:-:server.ccl.net>
To: CCL
Subject: CCL: iPhone & iPad 3D Molecule Browser - iMolview
Message-Id: <-44599-110509025921-2264-dWCGBnZuHzYd13yVFqurZQ:-:server.ccl.net>
X-Original-From: Tasaka Tomo <t.tasaka^_^gmail.com>
Content-Transfer-Encoding: 8bit
Content-Type: text/plain; charset=windows-1252
Date: Mon, 9 May 2011 15:59:12 +0900
MIME-Version: 1.0


Sent to CCL by: Tasaka Tomo [t.tasaka+/-gmail.com]
Hello,

there is "Load File (icb/pdb) From The Web" option in iMolview's Menu(v1.1).
so, it's possible to access my pdb files through the web server..

HTH
tomo


2011/5/7 Arne Dieckmann adieckma-$-googlemail.com <owner-chemistry~!~ccl.net>:
>
> Sent to CCL by: Arne Dieckmann [adieckma],[googlemail.com]
> Dear Andrew,
>
> how about loading in your own pdb files? I'd buy it if that will be possible.
>
>
> Cheers,
> Arne
>
>
> On May 7, 2011, at 2:13 AM, Andrew Orry andy:_:molsoft.com wrote:
>
>> Dear All,
>>
>> MolSoft is excited to announce the release of an iPhone and iPad app that lets you browse protein, DNA, and drug molecules in 3D. The app has a direct link to the Protein Data Bank (PDB) and DrugBank and has a fast and easy to use interface. Touching the molecules via the screen allows you to interact immediately with the 3D structures in a unique way. You can zoom in and out, rotate, spin, pan, and clip the 3D molecules with your finger tips in ways that are impossible using a traditional mouse and desktop computer.
>>
>> For more details and screenshots see: http://www.molsoft.com/iMolview.html
>>
>> The key features are:
>>       • Easy to use touch interface.
>>       • A direct link to the Protein Data Bank (PDB) and DrugBank.
>>       • Each molecular view can be customized with a rich set of molecular representations including: wires, balls-and-sticks, space filling, ribbon diagrams, and molecular surfaces.
>>       • Zoom in and out, rotate, spin, pan, and clip the 3D molecule.
>>       • A wide selection of coloring schemes is available.
>>       • Color background, color molecule by atom type, chain, N- to C- terminal, and secondary structure.
>>       • Select residues, atoms, or chains and color or change their representations individually.
>>       • Select residues in sequence and get the corresponding selection in 3D.
>>       • Select the whole chain by holding the corresponding tab.
>>       • Display fog effect.
>>       • Set 'inertia' to the maximum and let your molecule spin in 3D indefinitely.
>>       • Display residue and site labels for the whole object or selection.
>>       • Direct link to PubMed.
>>       • Read in your own MolSoft ICM *.icb files.
>> We hope you enjoy using the app and find it useful for your research and teaching. We welcome any feedback you may have.
>>
>> Thanks,
>> Andrew
>> --
>> Andrew Orry Ph.D.
>> MolSoft LLC
>> Senior Research Scientist
>> 11199 Sorrento Valley Road, S209
>> San Diego
>> CA 92121
>> Tel: 858-625-2000 x108
>> Fax: 828-625-2888
>>
>> www.molsoft.com>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt>
>
>


From owner-chemistry@ccl.net Mon May  9 09:46:00 2011
From: "uekstrom(0)gmail.com uekstrom(0)gmail.com" <owner-chemistry],[server.ccl.net>
To: CCL
Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN?
Message-Id: <-44600-110509085218-25946-DweIQ4W+E7gFa82h9Nsgvw],[server.ccl.net>
X-Original-From: "uekstrom*gmail.com" <uekstrom*gmail.com>
Content-Type: text/plain; charset=ISO-8859-1
Date: Mon, 9 May 2011 14:52:07 +0200
MIME-Version: 1.0


Sent to CCL by: "uekstrom~~gmail.com" [uekstrom~~gmail.com]
Dear Michel,

> If you really got tridimensional arrays from calling routines, you can
> declare them as A(N*N*4) or A(*) in your own routines.

Sure, I was just explaining the packing.

> Did you try that and does it save execution time ?

I do know that my data is one contiguous in memory, so I don't see how
declaring the array differently would help. It's about access patterns
during multiplication, the original designer did not have this in
mind. But as you say, this is not strictly a Fortran problem, more a
typical problem of typical Fortran (77?) programs.

> Regarding the change of format N,N,4 vs. 4,N,N: each time that you
> decide about a format, you must decide to access to your structure via
> a specific set routines, and ONLY through these routines.

You are right, but then you lose all the much touted advantages of
Fortran matrix notation. A lot of people advocate "F77 with allocate",
which means that they will not use any opaque data structures.

> You can get garbage with any programming language, including C++,
> java, ADA, etc.

Absolutely, C++ is very bad in many ways, but at least it is a general
purpose language.

> It is not a matter of language: it is a matter of project management.

Partly, but each language carries with it a culture and a set of
practices, propagated through textbooks, ancient sources and oral
tradition. This is not so easy to change. I would very much like a
modern language for scientific computing, but the chances of that
every taking off is pretty slim (see how many people use Sun/Oracle
Fortress, for example).

Ulf


From owner-chemistry@ccl.net Mon May  9 11:07:00 2011
From: "Igor Filippov Contr igorf(_)helix.nih.gov" <owner-chemistry\a/server.ccl.net>
To: CCL
Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN?
Message-Id: <-44601-110509110132-19827-XTg0WNmpbUjQIHqK0nsZgQ\a/server.ccl.net>
X-Original-From: "Igor Filippov [Contr]" <igorf-*-helix.nih.gov>
Content-Transfer-Encoding: 7bit
Content-Type: text/plain; charset="UTF-8"
Date: Mon, 9 May 2011 10:56:32 -0400
MIME-Version: 1.0


Sent to CCL by: "Igor Filippov [Contr]" [igorf\a/helix.nih.gov]
>  each time that you
> decide about a format, you must decide to access to your structure via
> a specific set routines, and ONLY through these routines. Just as for
> classes, if some change occurs, you only need to change the pack of
> dedicated routines.

If that's the case then what is the problem with indexing from 1 or 0?
Surely the get/set routines can modify the original index to whatever
flavor one likes...
I'm absolutely puzzled why the starting point of an index is even an
issue...

Igor


From owner-chemistry@ccl.net Mon May  9 14:08:00 2011
From: "Andras Borosy andras.borosy^givaudan.com" <owner-chemistry(~)server.ccl.net>
To: CCL
Subject: CCL: chemoinformatics
Message-Id: <-44602-110509093621-5476-O9+p9lcyjwp4GuSk7vJ/XA(~)server.ccl.net>
X-Original-From: Andras Borosy <andras.borosy|-|givaudan.com>
Content-Type: multipart/alternative; boundary="=_alternative 004AB40EC125788B_="
Date: Mon, 9 May 2011 15:35:40 +0200
MIME-Version: 1.0


Sent to CCL by: Andras Borosy [andras.borosy(-)givaudan.com]
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--=_alternative 004AB40EC125788B_=--


From owner-chemistry@ccl.net Mon May  9 14:43:00 2011
From: "Deepak Pradeep Thakur deepak.p.thakur.]_[.gmail.com" <owner-chemistry]_[server.ccl.net>
To: CCL
Subject: CCL:G: Regarding defects in Graphene using Gaussian
Message-Id: <-44603-110509121306-5661-CrBb7T2Hj1q2gv+hhBcqgg]_[server.ccl.net>
X-Original-From: "Deepak Pradeep Thakur" <deepak.p.thakur . gmail.com>
Date: Mon, 9 May 2011 12:13:03 -0400


Sent to CCL by: "Deepak Pradeep Thakur" [deepak.p.thakur[*]gmail.com]
Dear all,

I am trying to optimize and/or calculate the single point energy for graphene 
with defect (that is with one or more atoms missing).
However, I am not able to get the Single point energy.
Nor there is convergence after 5000 cycles or more.
Can any one tell me how to handle defects (that is few atoms unbonded) in 
Gaussian?

Any clue would be of great help.

Thanks and regards
Deepak Thakur


From owner-chemistry@ccl.net Mon May  9 15:18:00 2011
From: "karthikeyan m.karthikeyan]|[ncl.res.in" <owner-chemistry{}server.ccl.net>
To: CCL
Subject: CCL: Request for Web based Molecular Descriptors (Open Source)
Message-Id: <-44604-110509092336-9843-WGjVCRvdpdQjs7YULJcHcw{}server.ccl.net>
X-Original-From: karthikeyan <m.karthikeyan]_[ncl.res.in>
Content-Transfer-Encoding: 8bit
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Date: Mon, 9 May 2011 18:52:47 +0530
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Sent to CCL by: karthikeyan [m.karthikeyan{}ncl.res.in]
I am interested to know open source based molecular descriptors  for
both 2D and 3D structures available in SMILES, SDF, MOL or any other
standard formats. Sometime back I used CDK, JOELib libraries to compute
descriptors for web based molecular descriptor calculations.

For example (Instructions URL :  http://tinyurl.com/6deudvf  )
Compute URL: http://moltable.ncl.res.in/web/guest/compute

I am yet to find opensource tools (command line - Win / Linux) to
compute QM / QC descriptors for single organic molecules. Using java JNI
we did some experiment on MOPAC program to compute descriptors
externally in a semi-automatic mode. So far we could calculate over 180
descriptors (CDK) and I am looking forward to more descriptors which are
usually used in QSAR, QSTR and QSPR related studies. Later this would be
extended to Ligand preparation for Target-Ligand related studies through
the web interface.

Any suggestions/collaboration welcome. Eventually all the opensource
tools / data would be made available for academic/public use through
MOLTABLE portal.


M.Karthikeyan
http://moltable.ncl.res.in/


Disclaimer:

This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/common/webmailDisclaimer.htm


From owner-chemistry@ccl.net Mon May  9 16:44:01 2011
From: "Erik-Jan Ras Erik-Jan.Ras],[avantium.com" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: Request for Web based Molecular Descriptors (Open Source)
Message-Id: <-44605-110509164250-12947-blmwIXlZWwMdPzxhHfSJ2w-*-server.ccl.net>
X-Original-From: Erik-Jan Ras <Erik-Jan.Ras**avantium.com>
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Date: Mon, 9 May 2011 22:41:29 +0200
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Sent to CCL by: Erik-Jan Ras [Erik-Jan.Ras{=}avantium.com]
You may want to try PaDel: http://padel.nus.edu.sg/software/padeldescriptor/

A reasonable overlap with the commercial package Dragon (based on the work of Todeschini)

Regards,
Erik-Jan


________________________________________
> From: owner-chemistry+erikjan.ras==avantium.com[a]ccl.net [owner-chemistry+erikjan.ras==avantium.com[a]ccl.net] On Behalf Of karthikeyan m.karthikeyan]|[ncl.res.in [owner-chemistry[a]ccl.net]
Sent: Monday, May 09, 2011 3:22 PM
To: Erik-Jan Ras
Subject: CCL: Request for Web based Molecular Descriptors (Open Source)

Sent to CCL by: karthikeyan [m.karthikeyan{}ncl.res.in]
I am interested to know open source based molecular descriptors  for
both 2D and 3D structures available in SMILES, SDF, MOL or any other
standard formats. Sometime back I used CDK, JOELib libraries to compute
descriptors for web based molecular descriptor calculations.

For example (Instructions URL :  http://tinyurl.com/6deudvf  )
Compute URL: http://moltable.ncl.res.in/web/guest/compute

I am yet to find opensource tools (command line - Win / Linux) to
compute QM / QC descriptors for single organic molecules. Using java JNI
we did some experiment on MOPAC program to compute descriptors
externally in a semi-automatic mode. So far we could calculate over 180
descriptors (CDK) and I am looking forward to more descriptors which are
usually used in QSAR, QSTR and QSPR related studies. Later this would be
extended to Ligand preparation for Target-Ligand related studies through
the web interface.

Any suggestions/collaboration welcome. Eventually all the opensource
tools / data would be made available for academic/public use through
MOLTABLE portal.


M.Karthikeyan
http://moltable.ncl.res.in/


Disclaimer:

This message and the information contained herein is proprietary and confidential and subject to the policy statement of the National Chemical Laboratory, Pune, India. You may review the policy at http://www.ncl-india.org/common/webmailDisclaimer.htmhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis email (including its attached files and other content) is confidential and intended only for the use by named addressee. Unauthorized use, dissemination, disclosure and/or copying are prohibited. This email, attachments and (any part of) its content are (1) intended for the named addressee(s) only, and (2) strictly confidential and proprietary. All rights are reserved by Avantium Holding B.V. and its subsidiaries ('Avantium'). Any unauthorized use, dissemination, disclosure and/or copying is strictly prohibited, except after prior and express written permission by Avantium. Avantium is not responsible for the correct transmission and timely receipt of this email and its content. Should you have received this email, attachments and its content by mistake, please bring this to our attention and destroy this email in full. Thank you. http://www.avantium.com/about/legal-disclaimer/


From owner-chemistry@ccl.net Mon May  9 18:14:00 2011
From: "Andrew Dalke dalke.%x%.dalkescientific.com" <owner-chemistry%x%server.ccl.net>
To: CCL
Subject: CCL: Program language in Quantum Chemistry: C++ or FORTRAN?
Message-Id: <-44606-110509173643-29587-RC7buUgoWb+fmXydE5uJ6A%x%server.ccl.net>
X-Original-From: Andrew Dalke <dalke .. dalkescientific.com>
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Date: Mon, 9 May 2011 23:36:29 +0200
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Sent to CCL by: Andrew Dalke [dalke{=}dalkescientific.com]
Michel, I can't help but notice your statements like:

> Oh I know, fortran is considered as garbage because there is the old
> "GOTO" statement. But GOTO is just a more powerful version of the
> "break" statement available in most modern languages.

and 

> Because teachers say that students are unable to understand C as first
> language, so, an "easier language is better for them", supposed to let
> students get the desired results faster than with other languages.

These are strawman arguments.

No one makes the first argument when comparing Fortran to C++.
For one, C++ also has goto statements.

The view that "students are unable to understand C as a first language"
is also not dominant nor even a significant minority viewpoint.

C, C++, Fortran, and such were not designed with new programmers
in mind. Basic, Pascal, and ABC are examples of languages which
were designed to be easier to learn, and to address questions like
"after a year of Python followed by Java, would students be more
capable at Java programming then if they had only done Java?"

One conference presentation I went to said that, based on
the improved test scores (the US Advanced Placement tests), the
answer is yes. Other more peer-reviewed articles back that up.

This might be surprising to know that Python drew heavily from
the academic research which went into the ABC research project,
and in the VPython teaching environment, both directed towards
how to make a language which is easier for beginners to learn.

Indeed, the surprising thing about Python is that it's relatively
easy to learn, but is also one that large numbers of
advanced software developers also enjoy using. (ABC, Basic,
Logo, and Tcl fail in the latter category.)


I also look at statements like these

> You can get garbage with any programming language, including C++,
> java, ADA, etc.


> I would recommand C as a jacknife for programming (and C++ is close to
> C, at least syntactically)

and wonder if you have any significant experience with Python,
Ruby, or any of the other dynamically typed languages.

That is, I can't see C as a "jackknife language" for anything
other than device drivers. Python, Ruby, Perl, and other
languages are more productive than C.

And here by "productive" I point you to the research of Lutz Prechelt

  An empirical comparison of C, C++, Java, Perl, Python, Rexx,
  and Tcl for a search/string-processing program
      http://page.mi.fu-berlin.de/prechelt/Biblio//jccpprtTR.pdf


which says in the abstract:

  The results indicate that, for the given programming problem,
  “scripting languages” (Perl, Python, Rexx, Tcl) are more
  productive than conventional languages. In terms of run time
  and memory consumption, they often turn out better than Java
  and not much worse than C or C++.

This is dated 10 March 2000, so the memory usage and runtime
numbers will have changed, but the overall trends, like the
"total time for programming" are still relevant.


Since you mentioned Python in:

> Some 30-40 years ago, it was said that BASIC had to be taught first,
> for the same reasons that python is taught first these recent years.

I'll first point out that 30-40 years ago people also said that:

- Lisp (or rather Scheme) had to be taught first (Steele and Sussman)
- Smalltalk had to be taught first (Alan Kay)
- Logo had to be taught first (Seymour Papert)

and the reasons are all the same - overall it's easier to teach
the general concepts of programmatic thought in languages which
are not Fortran and C. Or rather, in languages which have:

  - automatic memory management
  - first-class string data types (and here I mean Unicode string,
      not limited ASCII or 8-bit byte strings!)
  - range checking
  - tracebacks which report errors and the call stack
  - module systems (and not C's "compilation unit")
  - built in associative arrays and dynamically resizeable lists,
      but hopefully other more complex data containers

to which I would also add more modern capabilities like:

  - URL client handling
  - standard database interfaces (for example, a standard API
      for handling Oracle, SQLite, and MySQL, like Python's db-api2.0)
  - access to a modern GUI library like Qt (written in C++)
  - easy to build web servers (like Ruby on Rails)


On top of that, it would be great to have access to a large number of
people who are writing new libraries to handle things like:

  - regular expression libraries which aren't open to denial
      of service attacks (http://code.google.com/p/re2/)
  - direct access to GPU libraries which hook into the language's
      own memory management system (http://mathema.tician.de/software/pycuda)
  - potentially access to game frameworks like http://www.ogre3d.org/ .
      (Especially since they come with an existing layer for talking
       with a physics engine!)

or writing bindings between languages. For example, Python can:

 - talk to Fortran code via python-fortran (as Jerome Kieffer pointed out)
 - talk to R libraries via RPy
 - talk to C/C++ via Boost::Python, Swig, or several other toolkits
 - talk to C through Python's own foreign function interface


It shouldn't be surprising that someone who uses Python, Ruby,
Java or C++ (with Boost) and is used to working in this sort of
rich environment might not want to switch to Fortran as their
primary language.


> Fortran and C will undoubtly both survive during a long. A serious
> science programmer is welcome to learn both.


A serious science programmer is also welcome to learn C++,
Python, Java, and Javascript. Those are 30, 20, 16, and 16
years old, respectively, and show every sign of surviving
for at least the next 20 years. There's also R (18 years old
but it's an implementation of S from 36 years ago), and
Mathematica and Matlab if you want to go the commercial route.

(I put Javascript in there because you have to share your
data and analysis somehow.)

Lua is interesting if you want an embedded language in
your system. Think about embedding a different integrator
into your MD program at run-time, where the new integrator
is read from a script file! Lua's JIT should be able to
do that with minimal performance or memory overhead.

Haskell looks like an interesting language for heavy graph
theory work - I've wondered if it would be an exceptionally
good language for implementing graph canonicalization.

APL is also interesting, and the modern variant "J" is
freely available under the GPL from
 http://www.jsoftware.com/source.htm



				Andrew
				dalke++dalkescientific.com


From owner-chemistry@ccl.net Mon May  9 18:49:00 2011
From: "Jean Jules FIFEN julesfifen,,gmail.com" <owner-chemistry,+,server.ccl.net>
To: CCL
Subject: CCL:G: MO6
Message-Id: <-44607-110509155851-9320-qejoaJp4Cd8R3rNB2pHUVw,+,server.ccl.net>
X-Original-From: Jean Jules FIFEN <julesfifen() gmail.com>
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Date: Mon, 9 May 2011 20:58:38 +0100
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Sent to CCL by: Jean Jules FIFEN [julesfifen*gmail.com]
--00221532ced8f6bfa704a2dd4362
Content-Type: text/plain; charset=ISO-8859-1

Dear Sujit,
I would also want to precise that M06 is well appropriated for metallic and
non-metallic compounds, whereas M06-2X is only parameterized for
non-metallic compounds. Be aware of this information in order to fix what I
said before.

Best regards,

On 4 May 2011 18:47, Jean Jules FIFEN julesfifen{:}gmail.com <
owner-chemistry::ccl.net> wrote:

> Dear Sujit,
> I think that,
> for the first and the third problem, you could first of all left down the
> keyword *maxcycle* and its argument.  Moreover, I think it is useless to
> add the keyword *scf=tight* since it is the default in G09. If this work,
> try reducing the argument of maxcycle for IRC to 50 or less. For opt
> calculations, I think that the key word maxcycle is rather *maxcycles*(see the manual).
> Relevant to the second problem, I am not sure that the Thrular functional
> M06 is appropriate for metal ions. But, M06-2X is appropriated.
> After doing this, if the problem is still present, remove the keyword cdiis
> to allow the program to use a combination of EDIIS and CDIIS.
> Hope this will help,
>
> Best regards,
>
> On 4 May 2011 05:33, Deepthi Jose deepthi,iisertvm.ac.in <
> owner-chemistry^^ccl.net> wrote:
>
>> Dear Sujit,
>> The functional is M06 (MZeroSix) not MO6.
>>
>>
>>
>> Regards
>> Deepthi
>>
>>
>> On Wed, May 4, 2011 at 5:05 AM, Sujit Kumar Mondal sujitharvard###
>> gmail.com <owner-chemistry###ccl.net> wrote:
>>
>>> *Hi all*
>>> *I am sujit, i am working with Gaussian-09 very recently(2months)/ can
>>> be described as a beginnner. I am very much using B3lyp hybrid-function for
>>> verious calculation such geometry opt, IRC, Scrf etc but recently i am
>>> facing problem with MO6 function for IRC calculation!! *
>>> *1)# MO6/6-311+G(d,p) IRC=(calcfc,maxcycle=1000)
>>> scf=(tight,maxcycle=1000,cdiis) showing me all the time* *syntax
>>> error!! can anyone tell me what kind of mistake I am making during my
>>> input command in the route section?*
>>> **
>>> *2)# MO6/6-311+G(d,p) opt scf=(tight, cdiis) for Fe+3 complex, link died
>>> couple of times after 30min of run!! I do not know the reason behind it,
>>> though b3lyp gave nice results,  anybody can suggest what will be the
>>> probable problem for this case?*
>>>
>>> *3)# MO6/6-311+G(d,p) opt=(calcall,maxcycle=600)
>>> scf=(tight,maxcycle=600,cdiis) Also I am having problem for frequency
>>> calculation using MO6, syntax error, please correct my mistake?*
>>> **
>>> *Looking forward for suggestions*
>>> **
>>> *Sujit*
>>> **
>>> **
>>>
>>
>>
>
>
> --
> Jean Jules FIFEN.
> University of Douala
> Faculty of Science
> Laboratoire de Physique Fondamentale.
>
>


-- 
Jean Jules FIFEN.
University of Douala
Faculty of Science
Laboratoire de Physique Fondamentale.

--00221532ced8f6bfa704a2dd4362
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable

Dear Sujit,<br>I would also want to precise that M06 is well appropriated f=
or metallic and non-metallic compounds, whereas M06-2X is only parameterize=
d for non-metallic compounds. Be aware of this information in order to fix =
what I said before.<br>
<br>Best regards,<br><br><div class=3D"gmail_quote">On 4 May 2011 18:47, Je=
an Jules FIFEN julesfifen{:}<a href=3D"http://gmail.com">gmail.com</a> <spa=
n dir=3D"ltr">&lt;<a href=3D"mailto:owner-chemistry::ccl.net">owner-chemistr=
y::ccl.net</a>&gt;</span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Sujit,<br>I =
think that,<br>for the first and the third problem, you could first of all =
left down the keyword <b>maxcycle</b> and its argument.=A0 Moreover, I thin=
k it is useless to add the keyword <b>scf=3Dtight</b> since it is the defau=
lt in G09. If this work, try reducing the argument of maxcycle for IRC to 5=
0 or less. For opt calculations, I think that the key word maxcycle is rath=
er <b>maxcycles</b> (see the manual).<br>

Relevant to the second problem, I am not sure that the Thrular functional M=
06 is appropriate for metal ions. But, M06-2X is appropriated.<br>After doi=
ng this, if the problem is still present, remove the keyword cdiis to allow=
 the program to use a combination of EDIIS and CDIIS.<br>

Hope this will help,<br><br>Best regards,<br><br><div class=3D"gmail_quote"=
>On 4 May 2011 05:33, Deepthi Jose deepthi,<a href=3D"http://iisertvm.ac.in=
" target=3D"_blank">iisertvm.ac.in</a> <span dir=3D"ltr">&lt;<a href=3D"mai=
lto:owner-chemistry%5E%5Eccl.net" target=3D"_blank">owner-chemistry^^ccl.ne=
t</a>&gt;</span> wrote:<br>

<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Dear Sujit,<br>Th=
e functional is M06 (MZeroSix) not MO6.<br><br><br><br>Regards<br>Deepthi<d=
iv>

<div></div><div><br><br><div class=3D"gmail_quote">On Wed, May 4, 2011 at 5=
:05 AM, Sujit Kumar Mondal sujitharvard###<a href=3D"http://gmail.com" targ=
et=3D"_blank">gmail.com</a> <span dir=3D"ltr">&lt;<a>owner-chemistry###ccl.=
net</a>&gt;</span> wrote:<br>


<blockquote class=3D"gmail_quote" style=3D"border-left: 1px solid rgb(204, =
204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><b>Hi all</b=
></div>
<div><b>I am sujit, i am working with=A0Gaussian-09 very recently(2months)/=
 can be described as a beginnner. I am very much using B3lyp hybrid-functio=
n for verious calculation such geometry opt, IRC, Scrf etc but recently i a=
m facing problem with MO6 function for IRC calculation!! </b></div>




<div><b>1)# MO6/6-311+G(d,p) IRC=3D(calcfc,maxcycle=3D1000) scf=3D(tight,ma=
xcycle=3D1000,cdiis) showing me all the time</b> <b><font color=3D"#ff0000"=
>syntax error!!=A0</font><font color=3D"#000000">can anyone tell me what ki=
nd of mistake I am=A0making during my input command in the route section?</=
font></b></div>




<div><b></b>=A0</div>
<div><b>2)# MO6/6-311+G(d,p) opt scf=3D(tight, cdiis) for Fe+3 complex,=A0l=
ink died couple of times after 30min of run!! I do not know the reason behi=
nd it, though b3lyp gave nice results, =A0anybody can suggest what will be =
the probable=A0problem for this case?</b></div>




<div>=A0</div>
<div><b>3)# MO6/6-311+G(d,p) opt=3D(calcall,maxcycle=3D600) scf=3D(tight,ma=
xcycle=3D600,cdiis)=A0Also=A0I am having problem for frequency calculation =
using MO6, <font color=3D"#cc0000">syntax error, please correct my mistake?=
</font></b></div>




<div><b><font color=3D"#cc0000"></font></b>=A0</div>
<div><b><font color=3D"#cc0000">Looking forward for suggestions</font></b><=
/div>
<div><b><font color=3D"#cc0000"></font></b>=A0</div><font color=3D"#888888"=
>
<div><b><font color=3D"#cc0000">Sujit</font></b></div>
<div><b></b>=A0</div>
<div><b></b>=A0</div>
</font></blockquote></div><br>
</div></div></blockquote></div><br><br clear=3D"all"><br>-- <br><div dir=3D=
"ltr"><font size=3D"4"><span style=3D"color: rgb(51, 102, 255);">Jean Jules=
 FIFEN.<br>University of Douala<br>Faculty of Science<br>Laboratoire de Phy=
sique Fondamentale.<br>

</span></font></div><br>
</blockquote></div><br><br clear=3D"all"><br>-- <br><div dir=3D"ltr"><font =
size=3D"4"><span style=3D"color: rgb(51, 102, 255);">Jean Jules FIFEN.<br>U=
niversity of Douala<br>Faculty of Science<br>Laboratoire de Physique Fondam=
entale.</span></font></div>
<br>

--00221532ced8f6bfa704a2dd4362--


From owner-chemistry@ccl.net Mon May  9 21:37:01 2011
From: "Kunal Roy kunalroy_in:-:yahoo.com" <owner-chemistry-*-server.ccl.net>
To: CCL
Subject: CCL: New paper on validation of QSPR models
Message-Id: <-44608-110509213014-23059-r3mbaxFFHjL9cEAd5MxYFA-*-server.ccl.net>
X-Original-From: Kunal Roy <kunalroy_in*o*yahoo.com>
Content-Type: multipart/alternative; boundary="0-1058477312-1304990999=:36392"
Date: Tue, 10 May 2011 06:59:59 +0530 (IST)
MIME-Version: 1.0


Sent to CCL by: Kunal Roy [kunalroy_in##yahoo.com]
--0-1058477312-1304990999=:36392
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****APOLOGY FOR MULTIPLE POSTING****
=C2=A0
New paper on validation of QSPR models
=C2=A0
Ojha PK, Mitra I, Das R, Roy K, Further exploring rm2 metrics for validatio=
n of QSPR models. Chemom Intell Lab Syst 107, 2011, 194-205, http://dx.doi.=
org/10.1016/j.chemolab.2011.03.011
=C2=A0
The role of different validation metrics (including classical metrics and d=
ifferent variants of rm2 metrics) in differentiating the good=E2=80=9D (pre=
dictive) models from the =E2=80=9Cbad=E2=80=9D (low predictive) models has =
been studied. Finally, a set of guidelines has been proposed for checking t=
he predictive quality of QSPR models.




Kunal Roy, Ph.D.=20
Associate Professor, Drug Theoretics and Cheminformatics Lab, Department of=
 Pharmaceutical Technology,=20
JADAVPUR UNIVERSITY, Kolkata 700 032 (INDIA)
Email : kroy[a]pharma.jdvu.ac.in , kunalroy_in[a]yahoo.com=C2=A0=C2=A0
URL :=C2=A0=C2=A0 http://sites.google.com/site/kunalroyindia/=C2=A0, http:/=
/www.jaduniv.edu.in/profile.php?uid=3D550=C2=A0=C2=A0
=C2=A0
=C2=A0
--0-1058477312-1304990999=:36392
Content-Type: text/html; charset=utf-8
Content-Transfer-Encoding: quoted-printable

<table cellspacing=3D"0" cellpadding=3D"0" border=3D"0" ><tr><td valign=3D"=
top" style=3D"font: inherit;"><DIV><FONT size=3D4 face=3D"times new roman, =
new york, times, serif">****APOLOGY FOR MULTIPLE POSTING****</FONT></DIV>
<DIV><FONT size=3D4 face=3D"times new roman, new york, times, serif"></FONT=
>&nbsp;</DIV>
<DIV><STRONG><FONT size=3D4 face=3D"times new roman, new york, times, serif=
">New paper on validation of QSPR models</FONT></STRONG></DIV>
<DIV><FONT size=3D4 face=3D"times new roman, new york, times, serif"></FONT=
>&nbsp;</DIV>
<DIV><FONT face=3D"times new roman, new york, times, serif"><FONT size=3D4>=
Ojha PK, Mitra I, Das R, Roy K, <SPAN style=3D"COLOR: black"><STRONG>Furthe=
r exploring <I>r<SUB>m</SUB><SUP>2</SUP> </I>metrics for validation of QSPR=
 models</STRONG>. <I>Chemom Intell Lab Syst</I> 107, 2011, 194-205, </SPAN>=
<SPAN style=3D"COLOR: black"><A href=3D"http://dx.doi.org/10.1016/j.chemola=
b.2011.03.011" rel=3Dnofollow target=3D_blank><SPAN><FONT color=3D#0000ff>h=
ttp://dx.doi.org/<SPAN>10.1016/j.chemolab.2011.03.011</SPAN></FONT></SPAN><=
/A></SPAN></FONT></FONT></DIV>
<DIV><SPAN style=3D"COLOR: black"><FONT size=3D4 face=3D"times new roman, n=
ew york, times, serif"></FONT></SPAN>&nbsp;</DIV>
<DIV><FONT face=3D"times new roman, new york, times, serif"><FONT size=3D4>=
The role of different validation metrics (including classical metrics and d=
ifferent variants of <I>r</I><SUB><I>m</I></SUB><SUP><I>2</I></SUP> metrics=
) in differentiating the good=E2=80=9D (predictive) models from the =E2=80=
=9Cbad=E2=80=9D (low predictive) models has been studied. Finally, a set of=
 guidelines has been proposed for checking the predictive quality of QSPR m=
odels.<!-- articleText --></FONT></FONT></DIV>
<DIV><BR><BR><BR></DIV>
<DIV><FONT color=3D#0000bf><FONT face=3D"times new roman"><STRONG><EM><FONT=
 size=3D4>Kunal Roy, <FONT size=3D2>Ph.D.</FONT></FONT></EM></STRONG> <BR><=
EM>Associate Professor</EM>, Drug Theoretics and Cheminformatics Lab, Depar=
tment of Pharmaceutical Technology, <BR><EM><STRONG>JADAVPUR UNIVERSITY</ST=
RONG></EM>, Kolkata 700 032 (INDIA)</FONT></FONT></DIV>
<DIV><FONT color=3D#0000bf><FONT face=3D"times new roman">Email : <A href=
=3D"mailto:kroy[a]pharma.jdvu.ac.in" rel=3Dnofollow target=3D_blank>kroy[a]phar=
ma.jdvu.ac.in</A> , <A href=3D"mailto:kunalroy_in[a]yahoo.com" rel=3Dnofollow=
 target=3D_blank>kunalroy_in[a]yahoo.com</A>&nbsp;&nbsp;</FONT></FONT></DIV>
<DIV><FONT face=3D"times new roman"><FONT color=3D#0000bf>URL :&nbsp;&nbsp;=
 </FONT><A href=3D"http://sites.google.com/site/kunalroyindia/" rel=3Dnofol=
low target=3D_blank><FONT color=3D#0000bf>http://sites.google.com/site/kuna=
lroyindia/</FONT></A><FONT color=3D#0000bf>&nbsp;, <A href=3D"http://www.ja=
duniv.edu.in/profile.php?uid=3D550" rel=3Dnofollow target=3D_blank>http://w=
ww.jaduniv.edu.in/profile.php?uid=3D550</A>&nbsp;&nbsp;</FONT></FONT></DIV>
<DIV><FONT face=3D"times new roman"><FONT color=3D#0000bf><B><SPAN style=3D=
"FONT-FAMILY: 'serif'; COLOR: black; FONT-SIZE: 11pt" lang=3DEN-GB></SPAN><=
/B></FONT></FONT>&nbsp;</DIV>
<DIV><FONT face=3D"times new roman"><FONT color=3D#0000bf></FONT>&nbsp;</DI=
V></FONT></td></tr></table>
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