http://www.few.vu.nl/~bickel

The title of his talk will be =93Stacked DNA-base Quartets: = Structure, Chemistry and Computational Intricacies=94.

Authors are invited to submit their = papers, written in English, of up to 10 pages, presenting the results of original research = or=20 innovative practical applications relevant to the workshop=20 topics.

Papers should be=20 prepared according to the rules of Procedia Computer=20 Science.=20

Formatting information see for = text/latex and for MSword. =

Papers should be submitted in = pdf or word file format. =

Paper submissions should be done electronically,=20 using=20 submission system on page:

http://www.iccs-meeting.org/iccs2010/papers/upload.php= =20

At least one author of an accepted paper must = register and=20 present the paper at the workshop. =

Full=20 paper submission: =20 1^st January , 2010

http://www.iccs-meeting.org/iccs2010/papers/upload.php=

Notification of acceptance: 15^th = February,=20 2010

Camera-ready papers: =20 1^st March, 2010

ORGANISERS OF WORKSHOP
Ponnadurai Ramasami and Henry Fritz Schaefer = III
Email: = 5cca*uom.ac.mu=20
------=_NextPart_000_0034_01CA7334.7289FD60-- From owner-chemistry@ccl.net Wed Dec 2 04:28:01 2009 From: "Sobia Ahsan Halim sobia_halim|*|yahoo.com" To: CCL Subject: CCL: Autodock re-rescoring Message-Id: <-40840-091202021428-11926-LK//S3dymCmbGoThZKchsw- -server.ccl.net> X-Original-From: "Sobia Ahsan Halim" Date: Wed, 2 Dec 2009 02:14:24 -0500 Sent to CCL by: "Sobia Ahsan Halim" [sobia_halim(-)yahoo.com] Dear All Hi Can any one please let me know how to rescore compounds using AutoDock. I have idea about docking on AutoDock but I dont have idea about rescoring of docked poses. Looking for reply. Thanks in advance. From owner-chemistry@ccl.net Wed Dec 2 05:05:00 2009 From: "manoj kumar manojrudraraju*gmail.com" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40841-091202004029-3203-lPUcNGyI31taDpz109UldA+*+server.ccl.net> X-Original-From: manoj kumar Content-Type: multipart/alternative; boundary=0016369c90719786f20479b78a30 Date: Wed, 2 Dec 2009 10:15:17 +0530 MIME-Version: 1.0 Sent to CCL by: manoj kumar [manojrudraraju#%#gmail.com] --0016369c90719786f20479b78a30 Content-Type: text/plain; charset=ISO-8859-1 Hi All, Does anyone aware or has developed any tool to retrieve Unique molecules > from a large compound databases. if not what would be the challenges ahead to develop such script, I wish to know the math behind such operation and want to develop in python. Thanks for read and time, regards Manoj --0016369c90719786f20479b78a30 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Hi All,

=A0

Does anyone aware or has developed any tool to retrieve Unique molecul= es from a large compound databases.

=A0

if not what would be the challenges ahead to develop such=A0 script, I= wish to know the math behind such operation and want to develop in python.=

=A0

Thanks for read and time,

=A0

regards

Manoj

=A0

--0016369c90719786f20479b78a30-- From owner-chemistry@ccl.net Wed Dec 2 05:34:01 2009 From: "Ye Qing yeqing ~ ihep.ac.cn" To: CCL Subject: CCL: Questions about the CPCM calculation Message-Id: <-40842-091202032750-24155-cvaocfg4VKboJcBhkRAXNA]|[server.ccl.net> X-Original-From: "Ye Qing" Date: Wed, 2 Dec 2009 03:27:45 -0500 Sent to CCL by: "Ye Qing" [yeqing ~ ihep.ac.cn] Sorry, the general used wavefunction symbol cann't be recognized by the mai system, so in the last mail, the expression of U(ion-water) should be U(ion-water)=(ion-water)-(ion)-(water); From owner-chemistry@ccl.net Wed Dec 2 09:48:01 2009 From: "andras.borosy_-_givaudan.com" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40843-091202055534-28616-sfdnNtxHobyD4rTIjrVxvw . server.ccl.net> X-Original-From: andras.borosy-$-givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 003BFF36C1257680_=" Date: Wed, 2 Dec 2009 11:55:20 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy(0)givaudan.com This is a multipart message in MIME format. --=_alternative 003BFF36C1257680_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Manoj, MOE from CCG (http://www.chemcomp.com/) does have it. Regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com "manoj kumar manojrudraraju*gmail.com" =20 Sent by: owner-chemistry+andras.borosy=3D=3Dgivaudan.com+*+ccl.net 02.12.2009 05:45 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: Tool or Software Module to retrieve unique molecules Hi All, =20 Does anyone aware or has developed any tool to retrieve Unique molecules=20 > from a large compound databases. =20 if not what would be the challenges ahead to develop such script, I wish=20 to know the math behind such operation and want to develop in python. =20 Thanks for read and time, =20 regards Manoj =20 =20 =20 =20 --=_alternative 003BFF36C1257680_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Manoj,

MOE = from CCG (http://www.chemcomp.com/) does have it.

Regards,

Dr. Andr=E1s P=E9ter Borosy
Scientific Modelling Expert

Fragrance Research
Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf - Switzerland
T:+41-44-824 2164 - F:+41-44-8242926 - http:= //www.givaudan.com

"manoj kumar man= ojrudraraju*gmail.com" <owner-chemistry+*+ccl.net>
Sent by: owner-chemistry+andras.boro= sy=3D=3Dgivaudan.com+*+ccl.net

02.12.2009 05:45

Please respond to
"CCL Subscribers" <chemistry+*+ccl.net>

To	"Borosy, Andras " <andras.borosy+*+givaudan.com>
cc
Subject	CCL: Tool or Software Module to retr= ieve unique molecules

Hi All,

Does anyone aware or has developed any tool to retrieve Unique molecules from a large compound databases.

if not what would be the challenges ahead to develop suc= h script, I wish to know the math behind such operation and want to develop in python.

Thanks for read and time,

regards
Manoj

--=_alternative 003BFF36C1257680_=-- From owner-chemistry@ccl.net Wed Dec 2 10:23:01 2009 From: "Matthias Wirth mawirth[a]gmx.net" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40844-091202090842-7222-BZWyLOHRPeRRpDR5s1aEIQ-.-server.ccl.net> X-Original-From: Matthias Wirth Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Wed, 2 Dec 2009 15:08:15 +0100 Mime-Version: 1.0 (Apple Message framework v1077) Sent to CCL by: Matthias Wirth [mawirth-$-gmx.net] Hi Manoj, How about having a unique SMILES representation (OpenBabel etc) of your = compounds and using the shell command: sort -u mysmiles.smi=20 or uniq mysmiles.smi Have fun, Matthias On Dec 2, 2009, at 5:45 AM, manoj kumar manojrudraraju*gmail.com wrote: > Hi All, >=20 > Does anyone aware or has developed any tool to retrieve Unique = molecules from a large compound databases. >=20 > if not what would be the challenges ahead to develop such script, I = wish to know the math behind such operation and want to develop in = python. >=20 > Thanks for read and time, >=20 > regards > Manoj >=20 >=20 >=20 >=20 From owner-chemistry@ccl.net Wed Dec 2 10:59:01 2009 From: "Wolf-D.Ihlenfeldt wdi[a]xemistry.com" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40845-091202065128-26034-ffvouW64MN7TXm0qGrrflA\a/server.ccl.net> X-Original-From: "Wolf-D.Ihlenfeldt" Content-Language: en-us Content-Type: multipart/alternative; boundary="----=_NextPart_000_001F_01CA734D.37A75670" Date: Wed, 2 Dec 2009 12:44:40 +0100 MIME-Version: 1.0 Sent to CCL by: "Wolf-D.Ihlenfeldt" [wdi,+,xemistry.com] This is a multi-part message in MIME format. ------=_NextPart_000_001F_01CA734D.37A75670 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable =20 Here is a minimal framework to copy unique records (as un-interpreted = byte images, so there are no reformatting problems) from a potentially huge = SD file (or other recognized format, this will automatically also work with SMILES, MOL2, RDF, etc) to standard output using a Cactvs toolkit script (www.xemistry.com, free for academic use): =20 ---snip--- set fh [molfile open =93myfile.sdf=94 r hydrogens add] molfile loop $fh eh { set hash [ens get $eh E_HASHISY] if {![info exists hashes($hash)]} { set hashes($hash) 1 molfile backspace $fh molfile copy $fh stdout } } ---snip--- =20 This script uses structure hashcodes (good ones, no known collisions, = they are for example the primary key in PubChem, this variant includes stereochemistry and isotope labels). =20 =20 =20 W. D. Ihlenfeldt Xemistry GmbH wdi _ xemistry.com Phone: +49 6174 201455 / Fax +49 6174 209665 --- xemistry gmbh =96 Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS 34-400-1719=20 =20 > From: owner-chemistry+wdi=3D=3Dxemistry.com _ ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com _ ccl.net] On Behalf Of = manoj kumar manojrudraraju*gmail.com Sent: Wednesday, December 02, 2009 5:45 AM To: Ihlenfeldt, Wolf D Subject: CCL: Tool or Software Module to retrieve unique molecules =20 Hi All, =20 Does anyone aware or has developed any tool to retrieve Unique molecules > from a large compound databases. =20 if not what would be the challenges ahead to develop such script, I = wish to know the math behind such operation and want to develop in python. =20 Thanks for read and time, =20 regards Manoj =20 =20 =20 =20 ------=_NextPart_000_001F_01CA734D.37A75670 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Here is a minimal framework to copy unique records (as = un-interpreted byte images, so there are no reformatting problems) from a potentially = huge SD file (or other recognized format, this will automatically also work with SMILES, MOL2, RDF, etc) to standard output using a Cactvs toolkit script = (www.xemistry.com, free for academic = use):

---snip---

set fh [molfile open “myfile.sdf” r hydrogens = add]

molfile loop $fh eh {

=A0 =A0=A0set hash [ens get $eh = E_HASHISY]

=A0=A0 =A0if {![info exists hashes($hash)]} = {

=A0=A0=A0=A0=A0 set hashes($hash) 1

=A0=A0=A0 =A0=A0molfile backspace = $fh

=A0=A0=A0=A0 =A0molfile copy $fh = stdout

=A0=A0}

}

---snip---

This script uses structure hashcodes (good ones, no known collisions, they are for example the primary key in PubChem, this = variant includes stereochemistry and isotope labels).

W. D. Ihlenfeldt
Xemistry GmbH
wdi _ xemistry.com

Phone: +49 6174 201455 / Fax +49 6174 209665
---
xemistry gmbh – Gesch=E4ftsf=FChrer/Managing Director: Dr. W. D. = Ihlenfeldt
Address: Hainholzweg 11, D-61462 K=F6nigstein, Germany
HR K=F6nigstein B7522 : Ust/VAT ID DE215316329 : DUNS = 34-400-1719

From:= owner-chemistry+wdi=3D=3Dxemistry.com _ ccl.net [mailto:owner-chemistry+wdi=3D=3Dxemistry.com _ ccl.net] On Behalf Of = manoj kumar manojrudraraju*gmail.com
Sent: Wednesday, December 02, 2009 5:45 AM
To: Ihlenfeldt, Wolf D
Subject: CCL: Tool or Software Module to retrieve unique = molecules

Hi All,

Does anyone aware or has developed any tool to = retrieve Unique molecules from a large compound databases.

if not what would be the challenges ahead to = develop such script, I wish to know the math behind such operation and = want to develop in python.

Thanks for read and time,

regards

Manoj

------=_NextPart_000_001F_01CA734D.37A75670-- From owner-chemistry@ccl.net Wed Dec 2 11:34:00 2009 From: "Michel Petitjean petitjean.chiral#gmail.com" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40846-091202082301-3070-ii+tHa2knB4WMSV54aO/WA]|[server.ccl.net> X-Original-From: Michel Petitjean Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 2 Dec 2009 13:51:23 +0100 MIME-Version: 1.0 Sent to CCL by: Michel Petitjean [petitjean.chiral]^[gmail.com] I guess that there are implicit assupmtions here: - Compounds should be retrieved on the basis of their molecular graph rather than from their caretesian coordinates - The full molecule is to be searched, rather than a substructure (motif with free sites) - Also, no Markush formula, no unspecified atom type or unspecified bond type, etc. - Neglecting tautomery, mesomery, aromaticity problems, etc. - Neglecting charges and isotopes, charges, protonation problems, pH, etc. - Neglecting stereochemical constraints such as Z/E, R/S, etc. Then you have to program a graph isomorphism detection routine. It is highly suggested to operate on H-suppressed graphs. In some of the situations listed above, you would have need to enumerate all isomorphisms rather than exhibit the first one you find, before concluding that it is the same compound or not (the meaning of what is << the same compound >> must be stated). If you allow the existence of several connex components in the question and in the database, take care of what that means: is it a one to one correspondance to be found, or else (discarding the coefficients). If you are looking to search in a large database, you should first apply filters because the graph isomorphism routine is rather time consuming. Etc. To summarize, it is not a trivial task. Good luck. Michel Petitjean, CEA/DSV/iBiTec-S/SB2SM (CNRS URA 2096), 91191 Gif-sur-Yvette Cedex, France. Phone: +331 6908 4006 / Fax: +331 6908 4007 E-mail: michel.petitjean[-]cea.fr, petitjean.chiral[-]gmail.com (preferred) http://petitjeanmichel.free.fr/itoweb.petitjean.graphs.html ---------- Forwarded message ---------- > From: manoj kumar manojrudraraju*gmail.com Date: 2009/12/2 Subject: CCL: Tool or Software Module to retrieve unique molecules To: "Petitjean, Michel " Hi All, Does anyone aware or has developed any tool to retrieve Unique molecules from a large compound databases. if not what would be the challenges ahead to develop such script, I wish to know the math behind such operation and want to develop in python. Thanks for read and time, regards Manoj From owner-chemistry@ccl.net Wed Dec 2 12:11:00 2009 From: "Jozsef Csontos jcsontos.lists^_^gmail.com" To: CCL Subject: CCL: Reversed energies by HF and B3LYP Message-Id: <-40847-091202060506-3390-MYMxsYSTnoVgiynjM+AIMQ_-_server.ccl.net> X-Original-From: Jozsef Csontos Content-Type: multipart/alternative; boundary="------------030201000905080104040503" Date: Wed, 02 Dec 2009 11:38:19 +0100 MIME-Version: 1.0 Sent to CCL by: Jozsef Csontos [jcsontos.lists|gmail.com] This is a multi-part message in MIME format. --------------030201000905080104040503 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Hi, there is nothing surprising there. The HF method is an uncorrelated mean field approximation by definition and DFT includes some electron correlation and this can make a huge difference. You can conclude that electron correlation plays an important role (as expected) in the stabilization of your conformers. However, this doesn't mean that the B3LYP result is closer to reality than that of HF. You should find some independent facts which support one of your findings (experimental measurements, higher level calculations - some benchmark results for systems which are similar to yours ). Maybe you should do this kind of benchmarking using smaller model systems or basis sets. Anyway, my suggestion would be to 1, search the literature regarding the performance of functionals for your system of interest (or similar) maybe not B3LYP is the best choice 2, it can happens that DFT is not the way to go, try to use some efficient variants of MP2 (RI-,local, etc), if you can afford it 3, use substantially larger basis set than 6-31G* in the final calculations if you can afford it; you definitely need diffuse basis functions to deal with anionic systems Best, Jozsef On 12/01/2009 08:17 PM, Radoslaw Kaminski rkaminski.rk,gmail.com wrote: > Hi, > > It could be difference in methods themselfs. DFT takes more factors > into account than HF but that is not always the best thing (!). I > could suggest to do DFT calculations with some big basis set like > aug-cc-PVDZ for B3LYP, BP86 functionals. Also you could set up some > calculations with MP2 method, also with big basis set. I could mainly > trust such results so you could have some reference point for comparison. > > The point is what are you going to analyse anyway? If you want to do > quantitavie analysis I would go to MP2 with big basis sets and compare > them with DFT results. From my experiemce even if you use B3LYP with > 6-311++G** basis set it gives sometimes totally different results > (lack of one minium of energy!) compared to B3LYP/aug-cc-pVDZ which > was more or less the same as in MP2 calculation. > > Hope it helps, > > Radek > > > 2009/12/1 Sanghwa Han hansh^^^kangwon.ac.kr > > > > > Sent to CCL by: "Sanghwa Han" [hansh.:.kangwon.ac.kr > ] > Dear Collegues, > > I am trying to obtain energies of anionic phenyl sulfate > [C6H5-OSO3(-1)]conformers with the dihedral CC-OS of 0 and 90 degrees. > When the conformers were optimized by HF/6-31G*, the 0 degree > conformer had a higher (by 0.883 kJ/mol) energy than the 90 degree > conformer. > But single point energy calculations using B3LYP/6-31G* on the > optimized structures showed that the 90 degree conformer had a > higher (by 5.962 kJ/mol)energy than the 0 degree conformer. The > energies were reversed with a big difference in magnitude. > I tried other basis sets but always had reversed energies for B3LYP. > The 90 degree conformer appears to have a lower steric energy by a > visual inspection. > > Any comments on the matter would be appreciated. > > > > -= This is automatically added to each message by the mailing > script =- > > > > E-mail to subscribers: CHEMISTRY|-|ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST|-|ccl.net > or use> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > --------------030201000905080104040503 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 8bit Hi,

there is nothing surprising there. The HF method is an uncorrelated mean field approximation by definition and DFT includes some electron correlation and this can make a huge difference. You can conclude that electron correlation plays an important role (as expected) in the stabilization of your conformers. However, this doesn't mean that the B3LYP result is closer to reality than that of HF. You should find some independent facts which support one of your findings (experimental measurements, higher level calculations - some benchmark results for systems which are similar to yours ). Maybe you should do this kind of benchmarking using smaller model systems or basis sets.
Anyway, my suggestion would be to
1, search the literature regarding the performance of functionals for your system of interest (or similar) maybe not B3LYP is the best choice
2, it can happens that DFT is not the way to go, try to use some efficient variants of MP2 (RI-,local, etc), if you can afford it
3, use substantially larger basis set than 6-31G* in the final calculations if you can afford it; you definitely need diffuse basis functions to deal with anionic systems

Best,

Jozsef

On 12/01/2009 08:17 PM, Radoslaw Kaminski rkaminski.rk,gmail.com wrote:

Hi,

It could be difference in methods themselfs. DFT takes more factors into account than HF but that is not always the best thing (!). I could suggest to do DFT calculations with some big basis set like aug-cc-PVDZ for B3LYP, BP86 functionals. Also you could set up some calculations with MP2 method, also with big basis set. I could mainly trust such results so you could have some reference point for comparison.

The point is what are you going to analyse anyway? If you want to do quantitavie analysis I would go to MP2 with big basis sets and compare them with DFT results. From my experiemce even if you use B3LYP with 6-311++G** basis set it gives sometimes totally different results (lack of one minium of energy!) compared to B3LYP/aug-cc-pVDZ which was more or less the same as in MP2 calculation.

Hope it helps,

Radek

2009/12/1 Sanghwa Han hansh^^^kangwon.ac.kr <owner-chemistry|-|ccl.net>

Sent to CCL by: "Sanghwa Han" [hansh.:.kangwon.ac.kr]
Dear Collegues,

I am trying to obtain energies of anionic phenyl sulfate [C6H5-OSO3(-1)]conformers with the dihedral CC-OS of 0 and 90 degrees.
When the conformers were optimized by HF/6-31G*, the 0 degree conformer had a higher (by 0.883 kJ/mol) energy than the 90 degree conformer.
But single point energy calculations using B3LYP/6-31G* on the optimized structures showed that the 90 degree conformer had a higher (by 5.962 kJ/mol)energy than the 0 degree conformer. The energies were reversed with a big difference in magnitude.
I tried other basis sets but always had reversed energies for B3LYP.
The 90 degree conformer appears to have a lower steric energy by a visual inspection.

Any comments on the matter would be appreciated.

E-mail to subscribers: CHEMISTRY|-|ccl.net or use:
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--------------030201000905080104040503-- From owner-chemistry@ccl.net Wed Dec 2 12:44:01 2009 From: "Cristian Bologa cbologa__salud.unm.edu" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40848-091202061855-15380-ed08AOL+UMvUd2a7tvtIdQ _ server.ccl.net> X-Original-From: "Cristian Bologa" Content-Type: multipart/alternative; boundary="=__Part96BCC6EF.0__=" Date: Wed, 02 Dec 2009 04:18:23 -0700 Mime-Version: 1.0 Sent to CCL by: "Cristian Bologa" [cbologa/a\salud.unm.edu] This is a MIME message. If you are reading this text, you may want to consider changing to a mail reader or gateway that understands how to properly handle MIME multipart messages. --=__Part96BCC6EF.0__= Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Hi Manoj, =20 Between the main challenges I would mention salts, tautomers and stereochem= istry. Some commercial toolkits are already pretty good at dealing with = that, and some non-commercial ones are not perfect yet but they are = getting better with each version. =20 If you want to build your own application for non-commercial use, you = should probably look at the OEChem Python toolkit from OpenEye. Regards, ~Cristian =20 Cristian Bologa, Ph.D. Research Associate Professor, Division of Biocomputing, Univ. of New Mexico, School of Medicine, MSC11 6145, Research Incubator Building, 2703 Frontier NE, Albuquerque, NM 87131 tel: +1-505-272-6509 fax:+1-505-272-0238 >>> "manoj kumar manojrudraraju*gmail.com" = 12/1/2009 9:45 PM >>> Hi All, Does anyone aware or has developed any tool to retrieve Unique molecules = > from a large compound databases. if not what would be the challenges ahead to develop such script, I wish = to know the math behind such operation and want to develop in python. Thanks for read and time, regards Manoj --=__Part96BCC6EF.0__= Content-Type: text/html; charset=US-ASCII Content-Transfer-Encoding: quoted-printable Content-Description: HTML

Hi Manoj,

Between the main challenges I would mention salts, tautomers and = stereochemistry. Some commercial toolkits are already pretty good at = dealing with that, and some non-commercial ones are not perfect yet = but they are getting better with each version.

If you want to build your own application for non-commercial use, you = should probably look at the OEChem Python toolkit from OpenEye.

Regards,

~Cristian

Cristian Bologa, Ph.D.
Research Associate = Professor,

Division of Biocomputing,<= BR>Univ. of New Mexico, School of Medicine,
MSC11 6145, Research = Incubator Building,
2703 Frontier NE, Albuquerque, NM 87131
tel: = +1-505-272-6509
fax:+1-505-272-0238

>>> "manoj kumar manojrudraraju*gmail.com" <owner-chem= istry-#-ccl.net> 12/1/2009 9:45 PM >>>

Hi All,

Does anyone aware or has developed any tool to retrieve Unique = molecules from a large compound databases.

if not what would be the challenges ahead to develop such script, I = wish to know the math behind such operation and want to develop in = python.

Thanks for read and time,

regards

Manoj

--=__Part96BCC6EF.0__=-- From owner-chemistry@ccl.net Wed Dec 2 13:23:01 2009 From: "andras.borosy{=}givaudan.com" To: CCL Subject: CCL: software for conformational analysis for the small ligands Message-Id: <-40849-091202050802-16193-QmlFKoZrsOQqIfHqesF81g(_)server.ccl.net> X-Original-From: andras.borosy*givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 00345282C1257680_=" Date: Wed, 2 Dec 2009 10:31:30 +0100 MIME-Version: 1.0 Sent to CCL by: andras.borosy,+,givaudan.com This is a multipart message in MIME format. --=_alternative 00345282C1257680_= Content-Type: text/plain; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable Dear Andrey, >I am looking for software by which it's possible to analyse datasets of=20 conformations for small molecule >comounds and select most probable=20 conformations. The academic free licenses or free licenses soft is of main = >interest. Buy MOE from CCG (http://www.chemcomp.com/) also for this purpose! It may=20 not be free for non-profit users, but it must not be very expensive and=20 its support is excellent. Considering the fact that your time does not=20 cost zero, it will be a good investment. I experiencened many times that=20 free things would be finally the most expensive. Best regards, Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http://www.givaudan.com --=_alternative 00345282C1257680_= Content-Type: text/html; charset="ISO-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Andrey,

>I am looking for software by which it's possible to analyse datasets of conformations for small molecule >comounds and select most probable conformations. The academic free licenses or free licenses soft is of main >interest. Buy MOE from CCG (http://www.chemcomp.com/) also for this purpose! It may not be free for non-profit users, but it must not be very expensive and its support is excellent. Considering the fact that your time does not cost zero, it will be a good investment. I experiencened many times that free things would be finally the most expensive.
Best regards,
Dr. Andr=E1s P=E9ter Borosy Scientific Modelling Expert Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf - Switzerland T:+41-44-824 2164 - F:+41-44-8242926 - http:= //www.givaudan.com --=_alternative 00345282C1257680_=-- From owner-chemistry@ccl.net Wed Dec 2 13:54:00 2009 From: "mo mohanine mohanine!=!gmail.com" To: CCL Subject: CCL:G: Gaussian scan/Opt Message-Id: <-40850-091202052932-3567-Ly2wGsETIRVEQ65vxdGksw=server.ccl.net> X-Original-From: "mo mohanine" Date: Wed, 2 Dec 2009 05:29:27 -0500 Sent to CCL by: "mo mohanine" [mohanine|a|gmail.com] Hi CCL community!!! I am using gaussian03. Satrting with an optimized planar geometry of a cyclique molecule I try to find minima and or TS a long the cycle opening path by scaning EPS with Opt=modredun keywords and increasing one bond with increment. Calculation is done with bond variation but without hole geometry reoptmiasation. I am asking how to setup commands to do the scan with geometry optimzation at each point of the scan. Thanks to all From owner-chemistry@ccl.net Wed Dec 2 14:28:01 2009 From: "Curt M Breneman brenec[]rpi.edu" To: CCL Subject: CCL: Web-based Cheminformatics Tools Message-Id: <-40851-091202111753-12346-fzj4V11CQTJequlnA00rZQ(a)server.ccl.net> X-Original-From: "Curt M Breneman" Date: Wed, 2 Dec 2009 11:17:50 -0500 Sent to CCL by: "Curt M Breneman" [brenec=rpi.edu] Dear Giuseppe, You may wish to try out our RECCR "ROMS" web application for exploring PLS, KPLS and SVM model building and validation. ROMS is freely available for use at http://reccr.chem.rpi.edu/Software/modeling/index.html. Other information about RECCR can be found at http://reccr.chem.rpi.edu , including other web-based and downloadable cheminformatics tools. Sincerely, Prof. Curt Breneman RPI Chemistry Director, RECCR Cheminformatics Center/ Rensselaer Cheminformatics Consortium From owner-chemistry@ccl.net Wed Dec 2 15:03:00 2009 From: "Jacco van de Streek vandestreek|a|avmatsim.de" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40852-091202111227-7608-TKJUA1UeCFFtb7agft0p7g%x%server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 02 Dec 2009 16:29:27 +0100 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [vandestreek,+,avmatsim.de] manoj kumar manojrudraraju*gmail.com wrote: > Does anyone aware or has developed any tool to retrieve Unique molecules > from a large compound databases. I am aware of projects that were done at the Cambridge Crystallographic Data Centre, but the computer programs that were used were in-house programs that work only on the Cambridge Structural Database. (Some references, but as I said these are for molecular crystal structures, although all comparisons were done solely on the molecular connectivities: J. van de Streek & S. Motherwell (2005). �GRX: a Program to Search the CSD for Functional Group Exchanges� J. Appl. Cryst. 38, 694-696. Compares molecules for equality after stripping user-specified pairs of functional groups, e.g. to find all instances where a -Cl has been replaced by a -Br. J. van de Streek (2007). �All Series of Multiple Solvates (Including Hydrates) from the Cambridge Structural Database� CrystEngComm 9, 350-352. Tries to find compound A with H2O, compound A with Benzene, compound A with chloroform etc. in a database, for all A. Acta Cryst. (2008). B64, 348-362 [ doi:10.1107/S0108768108005442 ] "Conformational variability of molecules in different crystal environments: a database study" Z. F. Weng, W. D. S. Motherwell, F. H. Allen and J. M. Cole In this paper, the conformational diversity of multiple occurrences of the same molecules in different crystal structures is extracted from a crystallographic database.) > if not what would be the challenges ahead to develop such script, I > wish to know the math behind such operation and want to develop in python. Some of the problems you will encounter (regardless which software you are using or whether you write your own): 1. Hydrogen atoms. In older crystallographic structures, hydrogens may not be present or wrongly assigned. In proteins, where the hydrogens were assigned may have been pH-dependent. And what is the convention for storing hydrochloric acid salts? Make sure your algorithm recognises that hydrogen and deuterium should match--or make it a flag whether or not they should match. Simply ignoring all hydrogens (i.e. by stripping them beforehand) probably does not work because e.g. acetic acid and an acetate ion are really different for most chemists, as are co-crystals versus salts. 2. Bond types (related to point 1. above and related to the question how you deal with charged species, which is related to point 6 below). Conjugated/aromatic/double bonds are not always assigned consistently (five-membered rings with two nitrogens are a nice example). Ignoring bond types completely is generally possible, but combined with ignoring all hydrogens is probably too much, so you may have to choose. If you can rely on your hydrogens, you can probably ignore your bond types. If you have a lot of metals in your compounds, even the assignment of bonds (I am not referring to bond types here, but to whether or not there is a bond at all) may be inconsistent. 3. Rings. Assigning R and S is easy, isn't it? You just look at the elements of the neighbours of the chiral atom, and if they are the same, you look at the neighbours' neighbours and so on. For 1-chloro-2,2-difluoro-cyclohexane that results in a nice infinite loop. Trivial to work around. Now let's say your algorithm tries to be clever and tries to analyse each compound to find all rings. How many rings are there in a buckyball? How many of them do you need to reconstruct your buckyball, i.e. which of them are "unique"? Which of them make sense to a chemist? (That would be all the five- and all the six-membered rings, but that means you are duplicating atoms, because in a buckyball the five- and six-membered rings are fused) What is the Smallest Set of Smallest Rings? You are sure you do not have buckyballs? What about steroids? 4. Stereochemistry. Are the R and the S version of two molecules the same or not? All of their physical properties are either identical or differ by a sign, and for structures determined by X-ray diffraction the assignment of R and S may be arbitrary. What about pure R, pure S and the corresponding racemate? Is there a flag to distinguish racemates > from enantiomerically pure compounds in your database? If not, are racemates stored as two connectivities (one for the R-form, one for the S-form)? Is the stereochemistry stored in the molecular connectivities (topologies) in your database in the first place? What about cis and trans? What about the R,R-form and the R,S-form, which are diastereomers and therefore chemically different species? 5. Exhaustive search versus single match. For your purpose, a single match suffices, make sure the algorithm is not trying to do an exhaustive search. Tert-butyl groups are a nice example: topologically, the three carbon atoms can match in 3! = 6 ways. For each of these 6 ways, each of the three methyl groups can be matched in 3! = 6 ways, so there are 3! * 3 * 3! = 108 ways to match them, I think. 6. Multiple "residues". Does each entry in your database contain exactly one 2D connectivity, or is it possible to have, say, a positively charged molecular ion with a chloride ion as the counter ion (as is usual for hydrochloric acid salts of drug compounds)? If so, what is compared? Does the chloride salt match the bromide salt? Should it? (I am pretty sure that a chemist that is searching for the chloride salt would be very pleased to know of the existence of the bromide salt, or of the neutral compound) What about solvents, like water, benzene? And if you are trying to be clever by ordering your residues by size before comparing two entries (to avoid having to compare all permutations) then remember that the R and the S form of a compound cannot be ordered unambiguously by size alone, and probably the same for all stereoisomers. When multiple residues are allowed, there is also the question of stoichiometry: if we write one molecule of compound A with one molecule of water as A:H20 = 1:1, then which of the following entries are the same: A:H20 = 1:1 compared to A:H20 = 1:2 ? (Same when dissolved in water) A:H20 = 1:1 compared to A:H20 = 1:0.98 ? A:H20 = 1:1 compared to A ? (Same when dissolved in water) 7. Speed. Assuming your equality measure is independent of the order of the two structures, to compare N entries you require (N*N-N)/2 comparisons. For the roughly 500,000 crystal structures in the Cambridge Structural Database, that is 125,000,000,000 comparisons. You will need a cheap (i.e. quick) initial screening method. For example, you can assign magic numbers (e.g. prime numbers) to each element and sum them over the non-hydrogen atoms in your chemical formulae (a more sophisticated approach is described in L. A. Evans, M. F. Lynch and P. Willett, J. Chem. Inf. Comput. Sci., 1978, 18, 146 and D. Bawden, J. T. Catlow, T. K. Devon, J. M. Dalton, M. F. Lynch and P. Willett, J. Chem. Inf. Comput. Sci., 1981, 21, 83). That gives you a large integer that you can use to do a quick and dirty initial screening--you can easily gain an order of magnitude speed up as compared to doing a full topological match. Hexane, cyclohexane and benzene would still be hits and would require a more careful (= slower) final examination. Since calculating these magic numbers may take time, you might consider creating a database for them on disk, or storing the matches from the initial screen on disk (in case you later find out you are not satisfied with your final screening method and you decide to redo the whole search). Best wishes, -- Dr Jacco van de Streek Senior Scientist Avant-garde Materials Simulation Freiburg im Breisgau, Germany From owner-chemistry@ccl.net Wed Dec 2 15:38:00 2009 From: "Curt Breneman brenec/a\rpi.edu" To: CCL Subject: CCL: Web servers for computer chemistry Message-Id: <-40853-091202111334-8997-VuxkDEQQpfR/RU88oDVRWQ*_*server.ccl.net> X-Original-From: "Curt Breneman" Content-Type: multipart/alternative; boundary="----=_NextPart_000_027C_01CA7336.B86DEB00" Date: Wed, 2 Dec 2009 10:03:37 -0500 MIME-Version: 1.0 Sent to CCL by: "Curt Breneman" [brenec+*+rpi.edu] This is a multi-part message in MIME format. ------=_NextPart_000_027C_01CA7336.B86DEB00 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit Dear Giuseppe, You may wish to try out our RECCR "ROMS" web application for exploring PLS, KPLS and SVM model building and validation. ROMS is freely available for use at http://reccr.chem.rpi.edu/Software/modeling/index.html. Other information about RECCR can be found at http://reccr.chem.rpi.edu , including other web-based and downloadable cheminformatics tools. Sincerely, Prof. Curt Breneman RPI Chemistry Director, RECCR Cheminformatics Center & Rensselaer Cheminformatics Consortium _____ > From: owner-chemistry+brenec==rpi.edu..ccl.net [mailto:owner-chemistry+brenec==rpi.edu..ccl.net] On Behalf Of qiancheng shen qianchengshen],[gmail.com Sent: Tuesday, December 01, 2009 8:51 PM To: Breneman, Curt Subject: CCL: Web servers for computer chemistry You may try www.dddc.ac.cn/some and www.dddc.ac.cn/admetus. They are all about prediction for ADMET properties of small molecules. 2009/12/1 Giuseppe Ermondi giuseppe.ermondi . unito.it Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi*_*unito.it] Dear CCL subscribers, I want to prepare some lessons about the use of the Web in molecular modeling and I am looking for web servers able to perform molecular mechanics and dynamic calculations and chemometrics analysis (PLS, PCA). The goal is to introduce molecular modeling thus it will be interesting educatonal web resources, too. Does anyone know web site with this features? Thanks in advance to all! Best regards, Giuseppe

Dear = Giuseppe,

You may wish to try out our RECCR = “ROMS” web application for exploring PLS, KPLS and SVM model building and = validation. ROMS is freely available for use at http://re= ccr.chem.rpi.edu/Software/modeling/index.html.

Other information about RECCR can = be found at http://reccr.chem.rpi.edu, including other web-based and downloadable cheminformatics = tools.

Sincerely,<= /p>

Prof. Curt Breneman

RPI = Chemistry

Director, RECCR Cheminformatics = Center & Rensselaer Cheminformatics = Consortium

From: = owner-chemistry+brenec=3D=3Drpi.edu..ccl.net [mailto:owner-chemistry+brenec=3D=3Drpi.edu..ccl.net] On Behalf Of qiancheng = shen qianchengshen],[gmail.com
Sent: Tuesday, December = 01, 2009 8:51 PM
To: Breneman, Curt =
Subject: CCL: Web servers = for computer chemistry

You may try www.dddc.ac.cn/some and www.dddc.ac.cn/admetus. They = are all about prediction for ADMET properties of small molecules. =

2009/12/1 Giuseppe Ermondi giuseppe.ermondi . unito.it <owner-chemistry|ccl.net>

Sent to CCL by: "Giuseppe Ermondi" [giuseppe.ermondi*_*unito.it]
Dear CCL subscribers,

I want to prepare some lessons about the use of the Web in = molecular modeling
and I am looking for web servers able to perform molecular mechanics = and
dynamic calculations and chemometrics analysis (PLS, PCA). The goal is = to
introduce molecular modeling thus it will be interesting educatonal = web
resources, too. Does anyone know web site with this features?

Thanks in advance to all!

Best regards,

Giuseppe

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------=_NextPart_000_027C_01CA7336.B86DEB00-- From owner-chemistry@ccl.net Wed Dec 2 16:19:01 2009 From: "Roberto Olivares-Amaya olivares * fas.harvard.edu" To: CCL Subject: CCL: Tool or Software Module to retrieve unique molecules Message-Id: <-40854-091202141525-31103-+B9LyJaL94XpOt5f2i/kcQ-.-server.ccl.net> X-Original-From: Roberto Olivares-Amaya Content-Type: multipart/alternative; boundary=000feaead813015b770479c22e45 Date: Wed, 2 Dec 2009 12:26:29 -0500 MIME-Version: 1.0 Sent to CCL by: Roberto Olivares-Amaya [olivares%x%fas.harvard.edu] --000feaead813015b770479c22e45 Content-Type: text/plain; charset=ISO-8859-1 Hello: Molgrep, which is part of perlmol is quite successful at doing that given a SMARTS pattern, which could be your specific molecule. We currently work with that with pretty good results. Here is a link to it. http://www.perlmol.org/examples/molgrep/ Roberto -- Roberto Olivares-Amaya Aspuru-Guzik Group Dept. of Chemistry and Chemical Biology Harvard University http://aspuru.chem.harvard.edu On Wed, Dec 2, 2009 at 9:08 AM, Matthias Wirth mawirth[a]gmx.net < owner-chemistry ~ ccl.net> wrote: > > Sent to CCL by: Matthias Wirth [mawirth-$-gmx.net] > Hi Manoj, > > How about having a unique SMILES representation (OpenBabel etc) of your > compounds and using the shell command: > > sort -u mysmiles.smi > > or > > uniq mysmiles.smi > > > Have fun, > > Matthias > > > On Dec 2, 2009, at 5:45 AM, manoj kumar manojrudraraju*gmail.com wrote: > > > Hi All, > > > > Does anyone aware or has developed any tool to retrieve Unique molecules > from a large compound databases. > > > > if not what would be the challenges ahead to develop such script, I wish > to know the math behind such operation and want to develop in python. > > > > Thanks for read and time, > > > > regards > > Manoj > > > > > > > > > > > > - This is automatically added to each message by the mailing script -> > -- Roberto Olivares-Amaya Aspuru-Guzik Group Dept. of Chemistry and Chemical Biology Harvard University http://aspuru.chem.harvard.edu --000feaead813015b770479c22e45 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hello:
Molgrep, which is part of perlmol is quite successful at doing th= at given a SMARTS pattern, which could be your specific molecule. We curren= tly work with that with pretty good results.
Here is a link to it.

http://www.perlmol= .org/examples/molgrep/

Roberto
--
Roberto Olivares-Amaya<= br>Aspuru-Guzik Group
Dept. of Chemistry and Chemical Biology
Harvard= University
http://aspuru.chem.harvard.edu

On Wed, Dec 2, 2009 at 9:08 AM, Matthias W= irth mawirth[a]gmx.net <= ;owner-chemistry ~ ccl.net>= wrote:

Sent to CCL by: Matthias Wirth [mawirth-$-gmx.net]
Hi Manoj,

How about having a unique SMILES representation (OpenBabel etc) of your com= pounds and using the shell command:

=A0 =A0 =A0 =A0sort -u mysmiles.smi

or

=A0 =A0 =A0 =A0uniq mysmiles.smi

Have fun,

=A0 =A0 =A0 =A0Matthias

On Dec 2, 2009, at 5:45 AM, manoj kumar manojrudraraju*gmail.com wrote:

> Hi All,
>
> Does anyone aware or has developed any tool to retrieve Unique molecul= es from a large compound databases.
>
> if not what would be the challenges ahead to develop such =A0script, I= wish to know the math behind such operation and want to develop in python.=
>
> Thanks for read and time,
>
> regards
> Manoj
>
>
>
>

- This is automatically added to each message by the mailing script -
E-mail to subscribers: CHEMISTRY ~ ccl.n= et or use:
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--
Roberto Oli= vares-Amaya
Aspuru-Guzik Group
Dept. of Chemistry and Chemical Biolog= y
Harvard University
http:= //aspuru.chem.harvard.edu
--000feaead813015b770479c22e45-- From owner-chemistry@ccl.net Wed Dec 2 16:49:00 2009 From: "Ronald C Bakus rbakus]*[chem.ucsb.edu" To: CCL Subject: CCL:G: Questions about linear dependence and basis set Message-Id: <-40855-091202164753-11427-fh1ZCi+j4gZsvO4qTr/p7w]-[server.ccl.net> X-Original-From: "Ronald C Bakus" Date: Wed, 2 Dec 2009 16:47:49 -0500 Sent to CCL by: "Ronald C Bakus" [rbakus(_)chem.ucsb.edu] Ol Ga, For the input I gave you, it completes one SCF cycle, and then fails to converge on the second, even with scf=nosymm (and along with scf=xqc) and ub3lyp. Im using G03 Rev E.01. Thanks, Ron > "Ol Ga eurisco1:-:pochta.ru" wrote: > > Sent to CCL by: "Ol Ga" [eurisco1===pochta.ru] > Dear Ronald C. Bakus, > > I used geometry posted by you earlier but I changed slightly route - I changed method to unrestricted (Ub3lyp). Also, I recommend to add NoSymm. I observed smooth SCF-convergence before XQC began to performe. > > Cycle 15 Pass 1 IDiag 1: > RMSU= 6.17D-09 CP: 6.72D-01 7.68D-01 9.51D-01 5.80D-01 7.61D-01 > CP: 7.40D-01 9.08D-01 9.12D-01 8.16D-01 8.60D-01 > CP: 8.93D-01 8.18D-01 7.10D-01 8.90D-01 > E= -1117.18461578981 Delta-E= 0.000000000079 Rises=F Damp=F > DIIS: error= 1.15D-08 at cycle 15 NSaved= 15. > NSaved=15 IEnMin=13 EnMin= -1117.18461578993 IErMin=15 ErrMin= 1.15D-08 > ErrMax= 1.15D-08 EMaxC= 1.00D-01 BMatC= 2.74D-13 BMatP= 2.88D-12 > IDIUse=1 WtCom= 1.00D+00 WtEn= 0.00D+00 > Coeff-Com: -0.140D-06 0.330D-06 0.303D-05 0.392D-05 0.829D-05 0.102D-04 > Coeff-Com: -0.102D-03-0.495D-03-0.180D-02-0.238D-02 0.363D-02 0.175D-01 > Coeff-Com: 0.164D+00 0.285D+00 0.535D+00 > Coeff: -0.140D-06 0.330D-06 0.303D-05 0.392D-05 0.829D-05 0.102D-04 > Coeff: -0.102D-03-0.495D-03-0.180D-02-0.238D-02 0.363D-02 0.175D-01 > Coeff: 0.164D+00 0.285D+00 0.535D+00 > Gap= 0.111 Goal= None Shift= 0.000 > Gap= 0.111 Goal= None Shift= 0.000 > RMSDP=4.49D-09 MaxDP=2.30D-07 DE= 7.87D-11 OVMax= 1.03D-07 > > SCF Done: E(UB3LYP) = -1117.18461579 A.U. after 15 cycles > Convg = 0.4487D-08 -V/T = 2.0098 > = 0.0000 = 0.0000 = 0.0000 = 0.0000 S= 0.0000 > = 0.000000000000E+00 > KE= 1.106300942892D+03 PE=-6.771451539404D+03 EE= 2.455058951308D+03 > Annihilation of the first spin contaminant: > S**2 before annihilation 0.0000, after 0.0000 > DiagDN has N= 672 LTot= 2048 but NE2= 3 cannot use DSYEVD. > Leave Link 502 at Tue Dec 1 08:49:35 2009, MaxMem= 131072000 cpu: 7983.5 > > QCSCF skips out because SCF is already converged. > > > What revision of Gaussian do you use? It is smart software. Thus, linear dependence can be observed very rarely. > > Sincerely, > > Ol Ga > > From owner-chemistry@ccl.net Wed Dec 2 18:18:00 2009 From: "Richard Harper drrwharper,gmail.com" To: CCL Subject: CCL: computational chemistry curriculum Message-Id: <-40856-091202181502-29355-jwvEbD6l3T/tDrEyjlHlaA~!~server.ccl.net> X-Original-From: Richard Harper Content-Type: multipart/alternative; boundary=000e0cd35648963fc70479c70ae5 Date: Wed, 2 Dec 2009 18:14:49 -0500 MIME-Version: 1.0 Sent to CCL by: Richard Harper [drrwharper|gmail.com] --000e0cd35648963fc70479c70ae5 Content-Type: text/plain; charset=ISO-8859-1 I am contemplating introduction of a module on computational chemistry into chemistry courses; possibly both graduate and undergraduate. Is there any sort of curriculum standard to guide the content of a course? What should be the expectations for teaching and learning? Thanks in advance, Dick --000e0cd35648963fc70479c70ae5 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable I am contemplating introduction of a module on computational chemistry into= chemistry courses; possibly both graduate and undergraduate.=A0 Is there a= ny sort of curriculum standard to guide the content of a course?=A0 What sh= ould be the expectations for teaching and learning?

Thanks in advance,
Dick
--000e0cd35648963fc70479c70ae5--