From owner-chemistry@ccl.net Thu Sep 20 09:14:00 2007 From: "Jan Labanowski janl]_[speakeasy.net" To: CCL Subject: CCL: IUPAC InChI/InChIKey project joins Microsoft BioIT Alliance Message-Id: <-35215-070920091241-3067-MVFOKb8Oy3pReD8PnUyFOA(a)server.ccl.net> X-Original-From: "Jan Labanowski" Date: Thu, 20 Sep 2007 09:12:37 -0400 Sent to CCL by: "Jan Labanowski" [janl=speakeasy.net] International Scientific Union joins with Microsoft and Life Science Industry Leaders to expedite Processes for Drug Discovery and Development The continued development of new and powerful medications for treatment of disease relies more and more heavily on collaborative projects, involving organizations possessing a wide range of complementary skills. The discovery techniques developed over many years by the pharmaceutical industry can now be married with a new generation of genome-based technologies, enabling many quite different approaches to maintaining personal health. Information technology is an integral part of this enterprise. The vast collections of biomedical data now emerging require ultra-sophisticated methods of data-handling, and such methods are currently being developed and improved by teams of software engineers in a variety of IT organizations. The establishment of the BioIT Alliance in April 2006 by Microsoft and leading organizations in the life science industries was very much a reflection of this scenario, and the Alliance has now been extended to include a major Scientific Union, the International Union of Pure and Applied Chemistry (IUPAC). The importance of IUPACs contribution to the enterprise lies primarily in the responsibility of this organization for establishing standards for transmitting chemical information. IUPAC has long been well known for its internationally agreed recommendations for deriving names for chemical substances. With the number of known substances running into many tens of millions, including both those reported in the scientific literature and those synthesized in-house, this is no mean achievement; however conventional names are not best suited to the age of information technology, and IUPAC, in collaboration with the US National Institute of Standards and Technology, has developed the machine-readable International Chemical Identifier (InChI), an open-source identifier algorithmically generated from a two-dimensional graphical structure (see http://iupac.org/inchi). This contains full structural information and can be converted back into the original structure. On September 5th 2007 IUPAC launched the beta-version of software to generate a new fixed-length (25-character) identifier, derived algorithmically from InChI and known as InChIKey (see http://www.iupac.org/inchi/release102.html). Although this version of the identifier does not itself contain information about chemical structure, it will * facilitate web searching * allow development of a web-based InChI lookup service * permit an InChI representation to be stored in fixed length fields * make chemical structure database indexing easier * allow verification of InChI character strings after network transmission. Stephen Heller (IUPAC Division of Chemical Nomenclature and Structure Representation) says: "The InChI/InChIKey is the first publicly available unique chemical identifier. Until IUPAC developed the InChI/InChIKey, it had not been possible to link and exchange information and data between the vast chemical world and the Life Sciences world that the Microsoft BioIT Alliance supports. The InChI/InChIKey is like a Digital Object Identifier (DOI) for chemicals. The InChI/InChIKey is an agent of change and an agent of the future for linking the chemical, biochemical, and biomedical information and data on the web. The InChI/InChIKey provides the Microsoft BioIT Alliance with a unique, easy, accurate, universal, and free way to link the information they collect and use internally and provide externally to their customers. The InChI/InChIKey provides the missing link between the chemical world and the Life Sciences world. I am very pleased that I am part of the team that has been able to put this one small but vital link in place to support and enhance drug discovery and improve the health of all persons around the world." According to Rudy Potenzone, Microsoft's Director of the BioIT Alliance and Industry Strategist for Life Sciences, "Microsoft is pleased to have IUPAC, the international chemistry standards organization, join the Microsoft BioIT Alliance. The IUPAC InChI/InChIKey is a critical link in making the goal of improving biomedical data interchange come to fruition in the near future. As more companies and organizations use the IUPAC InChI/InChIKey to connect information the international scientific community will benefit. We hope their participation in the Alliance can help expand its usage." About the BioIT Alliance Formed in 2006, the BioIT Alliance is a cross-industry group working to integrate science and technology in order to accelerate the pace of drug discovery and realize the potential of personalized medicine. Founding members include Accelrys Software Inc., Affymetrix, Inc., Agilent Technologies Inc., Amylin Pharmaceuticals, Inc., Applied Biosystems, The BioTeam Inc., Digipede Technologies LLC, Discovery Biosciences Corporation, Geospiza Inc., Hewlett-Packard Development Company, L.P., Illumina Inc., InterKnowlogy, Microsoft Corporation, Sun Microsystems Inc., The Scripps Research Institute, VizX Labs LLC and other key companies in the pharmaceutical, biotech, hardware and software industries. Additional information about the BioIT Alliance can be found on the BioIT Alliance Web site at http://www.bioitalliance.org. About the International Union of Pure and Applied Chemistry (IUPAC) The International Union of Pure and Applied Chemistry (IUPAC) exists to advance the worldwide aspects of the chemical sciences and to contribute to the application of chemistry in the service of mankind. As a scientific, international, non-governmental and objective body, IUPAC can address many global issues involving the chemical sciences. For more information see the IUPAC web site at http://www.iupac.org . From owner-chemistry@ccl.net Thu Sep 20 13:26:00 2007 From: "Kaci Tizi_Ouzou kaci.tiziouzou|*|gmail.com" To: CCL Subject: CCL: Mixing ECP and Basis sets: Message-Id: <-35216-070920115716-7386-Ar8y3x3jcImkGjYxGBxYag^^server.ccl.net> X-Original-From: "Kaci Tizi_Ouzou" Content-Type: multipart/alternative; boundary="----=_Part_32115_4333315.1190303439945" Date: Thu, 20 Sep 2007 09:50:39 -0600 MIME-Version: 1.0 Sent to CCL by: "Kaci Tizi_Ouzou" [kaci.tiziouzou|gmail.com] ------=_Part_32115_4333315.1190303439945 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi folks, I am trying to do a calculation on C2H4 adsobed on a Mo atom by mixing ECP and classical basis set. I did the following, #HF/GEN OPT Title 0 1 Mo C etc etc ... H C 0 6-31G(d) **** Mo 0 LANL2DZ <--- Core potential **** But I got a strange message: " Warning! Ti atom 1 has 43 valence electrons but only 22 basis functions. This is less than a minimal basis set!" I have no clue as to fixing the problem!!! Kass ------=_Part_32115_4333315.1190303439945 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Hi folks,
 
I am trying to do a calculation on C2H4 adsobed on a Mo atom by mixing ECP and classical basis set.
 
I did the following,
 
#HF/GEN OPT
 
Title
 
0 1
Mo
C
etc etc ... 
 
H C 0
6-31G(d)
****
Mo 0
LANL2DZ <--- Core potential
****
 
But I got a strange message:
 
" Warning! Ti atom 1 has 43 valence electrons but only 22 basis functions.
  This is less than a minimal basis set!"
 
I have no clue as to fixing the problem!!!
 
  
 
Kass
------=_Part_32115_4333315.1190303439945-- From owner-chemistry@ccl.net Thu Sep 20 14:16:01 2007 From: "Debellis Anthony CE US anthony.debellis{:}cibasc.com" To: CCL Subject: CCL:G: [CCL] RE: Mixing ECP and Basis sets: Message-Id: <-35217-070920141336-6480-SvwO3v9EYYlNm2dkATHRnw%x%server.ccl.net> X-Original-From: Debellis Anthony CE US Content-Class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7FBB1.AAD78615" Date: Thu, 20 Sep 2007 14:11:30 -0400 MIME-Version: 1.0 Sent to CCL by: Debellis Anthony CE US [anthony.debellis{=}cibasc.com] ------_=_NextPart_001_01C7FBB1.AAD78615 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable It looks like you have two problems here (I assume that you are using Gaussian) . The first is that it seems as if the program is interpreting the first two letters in the word "Title" as a specification of a titanium atom. I would try to give the run a meaningful title. The second is that by including the lines: Mo LANL2DZ you are not specifying a core potential but just the valence basis for molybdenum. To specify a core potential you must add the keyword "pseudo=3Dread" to the route section AND append a blank line followed = by: Mo LANL2DZ to your input file. In essence, you must specify "Mo" followed by "LANL2DZ" twice, once for the valence basis and another for the ECP. =20 Anthony =20 ________________________________ > From: owner-chemistry===ccl.net [mailto:owner-chemistry===ccl.net]=20 Sent: Thursday, September 20, 2007 11:51 AM To: Debellis Anthony CE US Subject: CCL: Mixing ECP and Basis sets: Hi folks, =20 I am trying to do a calculation on C2H4 adsobed on a Mo atom by mixing ECP and classical basis set. =20 I did the following, =20 #HF/GEN OPT =20 Title =20 0 1 Mo C etc etc ...=20 =20 H C 0 6-31G(d) **** Mo 0 LANL2DZ <--- Core potential **** =20 But I got a strange message:=20 =20 " Warning! Ti atom 1 has 43 valence electrons but only 22 basis functions. This is less than a minimal basis set!" =20 I have no clue as to fixing the problem!!! =20 =20 =20 Kass ------_=_NextPart_001_01C7FBB1.AAD78615 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable
It looks like you have two problems here (I = assume that=20 you are using Gaussian) .  The first is that it seems as if the = program is=20 interpreting the first two letters in the word "Title" as a = specification of a=20 titanium atom.  I would try to give the run a meaningful = title.  The=20 second is that by including the lines:
Mo
LANL2DZ
you are not specifying a core potential but = just the=20 valence basis for molybdenum.  To specify a core potential you must = add the=20 keyword "pseudo=3Dread" to the route section AND append a blank line = followed=20 by:
Mo
LANL2DZ
to your input file.  In essence, you = must specify=20 "Mo" followed by "LANL2DZ" twice, once for the valence basis and another = for the=20 ECP.
 
Anthony
 

From: owner-chemistry===ccl.net=20 [mailto:owner-chemistry===ccl.net]
Sent: Thursday, September = 20, 2007=20 11:51 AM
To: Debellis Anthony CE US
Subject: CCL: = Mixing ECP=20 and Basis sets:

Hi folks,
 
I am trying to do a calculation on C2H4 adsobed on a Mo atom = by mixing=20 ECP and classical basis set.
 
I did the following,
 
#HF/GEN OPT
 
Title
 
0 1
Mo
C
etc etc ... 
 
H C 0
6-31G(d)
****
Mo 0
LANL2DZ <--- Core potential
****
 
But I got a strange message:
 
" Warning! Ti atom 1 has 43 valence electrons but only 22 = basis=20 functions.
  This is less than a minimal basis set!"
 
I have no clue as to fixing the problem!!!
 
  
 
Kass
------_=_NextPart_001_01C7FBB1.AAD78615-- From owner-chemistry@ccl.net Thu Sep 20 16:37:01 2007 From: "Adam Tenderholt atenderholt]-[gmail.com" To: CCL Subject: CCL:G: [CCL] RE: Mixing ECP and Basis sets: Message-Id: <-35218-070920163102-21118-/MWbWL/AsRsw0laBZtNizA]-[server.ccl.net> X-Original-From: "Adam Tenderholt" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 20 Sep 2007 12:33:45 -0700 MIME-Version: 1.0 Sent to CCL by: "Adam Tenderholt" [atenderholt : gmail.com] To put it in a way that you can just copy into your input file, you need: H C 0 6-31G(d) **** Mo 0 LanL2DZ **** Mo 0 LanL2 The second part is for the ECP, so make sure you have pseudo=read in your route section. Also, make sure you have an empty line before and after the last ECP part. Adam On 9/20/07, Debellis Anthony CE US anthony.debellis{:}cibasc.com wrote: > > > It looks like you have two problems here (I assume that you are using > Gaussian) . The first is that it seems as if the program is interpreting > the first two letters in the word "Title" as a specification of a titanium > atom. I would try to give the run a meaningful title. The second is that > by including the lines: > Mo > LANL2DZ > you are not specifying a core potential but just the valence basis for > molybdenum. To specify a core potential you must add the keyword > "pseudo=read" to the route section AND append a blank line followed by: > Mo > LANL2DZ > to your input file. In essence, you must specify "Mo" followed by "LANL2DZ" > twice, once for the valence basis and another for the ECP. > > Anthony > > > ________________________________ > From: owner-chemistry_._ccl.net [mailto:owner-chemistry_._ccl.net] > Sent: Thursday, September 20, 2007 11:51 AM > To: Debellis Anthony CE US > Subject: CCL: Mixing ECP and Basis sets: > > > > Hi folks, > > I am trying to do a calculation on C2H4 adsobed on a Mo atom by mixing ECP > and classical basis set. > > I did the following, > > #HF/GEN OPT > > Title > > 0 1 > Mo > C > etc etc ... > > H C 0 > 6-31G(d) > **** > Mo 0 > LANL2DZ <--- Core potential > **** > > But I got a strange message: > > " Warning! Ti atom 1 has 43 valence electrons but only 22 basis functions. > This is less than a minimal basis set!" > > I have no clue as to fixing the problem!!! > > > > Kass From owner-chemistry@ccl.net Thu Sep 20 21:12:00 2007 From: "Green Power powergreen###gmail.com" To: CCL Subject: CCL: MOPAC problem Message-Id: <-35219-070920210928-29267-ni9WRYepUmChYWfkLaqFHw(a)server.ccl.net> X-Original-From: "Green Power" Content-Type: multipart/alternative; boundary="----=_Part_29573_33206934.1190336957380" Date: Thu, 20 Sep 2007 21:09:17 -0400 MIME-Version: 1.0 Sent to CCL by: "Green Power" [powergreen ~~ gmail.com] ------=_Part_29573_33206934.1190336957380 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All, I am trying to optimized the geometry of a charged molecule, which is supposed to be C2 symmetry. But the symmetry is broken for the optimized geometry. For the neutral molecule, it works well. The input file is listed as follows. Thank you in advance. Tian "PM6 Charge=-2 GNORM=0.05 6 Neutral C -0.253000000 -0.324600000 1.084900000 C 0.428300000 0.686500000 0.396100000 C 0.459700000 -1.065400000 2.112500000 C -0.067800000 1.288300000 -0.824400000 C 1.704500000 1.171700000 0.870900000 C -2.061300000 2.120700000 1.556500000 C 0.078600000 -2.337800000 2.472900000 C -2.701900000 -0.016500000 0.398000000 C -2.863800000 1.430500000 0.644100000 C -2.889400000 -2.868600000 0.173100000 C -1.614300000 -0.783600000 0.763200000 C -1.792500000 -2.244600000 0.910000000 C 1.644400000 -0.441900000 2.691000000 C 2.235700000 0.621700000 2.083200000 C -4.891400001 1.478100000 -0.795800000 C 2.397400000 2.177200000 0.156900000 C -1.009700000 -2.963300000 1.767100000 C -4.838300001 0.090000000 -0.878500000 C 0.633500000 2.251800000 -1.492200000 C -3.931800000 2.158000000 0.003800000 C -4.049000000 3.554900000 0.227600000 C -2.216000000 3.495700000 1.798700000 C -3.833800000 -0.662800000 -0.283200000 C 1.894800000 2.715700000 -1.008200000 C -3.848500000 -2.100200000 -0.393300000 C -3.195700000 4.210600001 1.110900000 H -1.280100000 1.583500000 2.100200000 H -1.030600000 0.936500000 -1.197200000 H -5.625000001 -0.423800000 -1.431900000 H 0.237400000 2.689000000 -2.403400000 H 0.589600000 -2.892400000 3.237300000 H 3.351800000 2.523700000 0.545400000 H -4.663900001 -2.551400000 -0.953800000 H -5.661300001 2.035100000 -1.294100000 H 3.128000000 1.077300000 2.503100000 H 2.420600000 3.482200000 -1.552300000 H 2.035800000 -0.868400000 3.603100000 H -1.556400000 3.990600000 2.496700000 H -1.178100000 -4.018100000 1.932200000 H -3.296500000 5.279000001 1.267700000 H -4.820600001 4.102500000 -0.292700000 H -2.895900000 -3.946400000 0.104500000" ------=_Part_29573_33206934.1190336957380 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear All,

I am trying to optimized the geometry of a charged molecule, which is supposed to be C2 symmetry. But the symmetry is broken for the  optimized geometry. For the neutral molecule, it works well. The input file is listed as follows. Thank you in advance.

Tian

"PM6 Charge=-2 GNORM=0.05
6
Neutral
C    -0.253000000     -0.324600000     1.084900000
C     0.428300000     0.686500000     0.396100000
C     0.459700000    -1.065400000     2.112500000
C    -0.067800000     1.288300000    -0.824400000
C     1.704500000     1.171700000      0.870900000
C    -2.061300000     2.120700000     1.556500000
C     0.078600000    -2.337800000     2.472900000
C    -2.701900000    -0.016500000     0.398000000
C    -2.863800000     1.430500000     0.644100000
C    -2.889400000    -2.868600000     0.173100000
C    -1.614300000    -0.783600000     0.763200000
C    -1.792500000    -2.244600000     0.910000000
C     1.644400000    -0.441900000     2.691000000
C     2.235700000     0.621700000     2.083200000
C    -4.891400001     1.478100000    -0.795800000
C     2.397400000     2.177200000     0.156900000
C    -1.009700000    -2.963300000     1.767100000
C    -4.838300001      0.090000000    -0.878500000
C     0.633500000     2.251800000    -1.492200000
C    -3.931800000     2.158000000     0.003800000
C    -4.049000000     3.554900000     0.227600000
C    -2.216000000     3.495700000      1.798700000
C    -3.833800000    -0.662800000    -0.283200000
C     1.894800000     2.715700000    -1.008200000
C    -3.848500000    -2.100200000    -0.393300000
C    -3.195700000     4.210600001     1.110900000
H    -1.280100000     1.583500000     2.100200000
H    -1.030600000     0.936500000    -1.197200000
H    -5.625000001    -0.423800000    -1.431900000
H     0.237400000     2.689000000    -2.403400000
H     0.589600000    -2.892400000     3.237300000
H     3.351800000     2.523700000     0.545400000
H    -4.663900001    -2.551400000    -0.953800000
H    -5.661300001     2.035100000    -1.294100000
H     3.128000000      1.077300000     2.503100000
H     2.420600000     3.482200000    -1.552300000
H     2.035800000    -0.868400000     3.603100000
H    -1.556400000     3.990600000     2.496700000
H    -1.178100000    -4.018100000      1.932200000
H    -3.296500000     5.279000001     1.267700000
H    -4.820600001     4.102500000    -0.292700000
H    -2.895900000    -3.946400000     0.104500000"
------=_Part_29573_33206934.1190336957380--