From owner-chemistry@ccl.net Mon Feb 16 01:58:00 2009 From: "Sangeetha Subramaniam srdshigella*gmail.com" To: CCL Subject: CCL: Chemical library analysis tool Message-Id: <-38624-090216015611-14869-oL/7SbLb0LeeO3AiIAYYzg]^[server.ccl.net> X-Original-From: Sangeetha Subramaniam Content-Type: multipart/alternative; boundary=000e0cd13bc29c49ae046303ad14 Date: Mon, 16 Feb 2009 11:25:55 +0430 MIME-Version: 1.0 Sent to CCL by: Sangeetha Subramaniam [srdshigella^gmail.com] --000e0cd13bc29c49ae046303ad14 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi all, Thanks a lot for the members who were so kind and generous in replying to my query. Best wishes Sangeetha. On Fri, Feb 13, 2009 at 6:25 PM, Igor Filippov Contr igorf#%#helix.nih.gov < owner-chemistry__ccl.net> wrote: > > Sent to CCL by: "Igor Filippov [Contr]" [igorf-.-helix.nih.gov] > Pipeline Pilot > > http://accelrys.com/products/scitegic/ > > Cheers, > Igor > > On Fri, 2009-02-13 at 06:25 -0500, Sangeetha Vimal > srdshigella-x-gmail.com wrote: > > Sent to CCL by: "Sangeetha Vimal" [srdshigella,gmail.com] > > Hi all, > > > > Can someone suggest me a chemical library analysis tool, which can help > in clustering/diversity analysis of chemical compounds in the database. > > > > Thanks > > Sangeetha> > -- > Igor Filippov [Contr] > > --000e0cd13bc29c49ae046303ad14 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi all,

Thanks a lot for the members who were so kind and generous <= br>in replying to my query.

Best wishes
Sangeetha.

On Fri, Feb 13, 2009 at 6:25 PM, Igor Filippov Contr ig= orf#%#helix.nih.gov = <owner-chemistry__ccl.net&= gt; wrote:

Sent to CCL by: "Igor Filippov [Contr]" [igorf-.-helix.nih.gov]
Pipeline Pilot

http:/= /accelrys.com/products/scitegic/

Cheers,
Igor

On Fri, 2009-02-13 at 06:25 -0500, Sangeetha Vimal
srdshigella-x-gmail.com wrote:
> Sent to CCL by: "Sangeetha  Vimal" [srdshigella,gmail.com]
> Hi all,
>
> Can someone suggest me a chemical library analysis tool, which can hel= p in clustering/diversity analysis of chemical compounds in the database. >
> Thanks
> Sangeetha>
--
Igor Filippov [Contr] <igorf^-^helix.nih.gov>



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--000e0cd13bc29c49ae046303ad14-- From owner-chemistry@ccl.net Mon Feb 16 03:56:01 2009 From: "Alexander Kos software[A]akosgmbh.eu" To: CCL Subject: CCL: Looking for SDF files for known toxic molecules Message-Id: <-38625-090215111612-23414-ADPZSnZBydNLOQx1ls+izg..server.ccl.net> X-Original-From: "Alexander Kos" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 15 Feb 2009 17:15:57 +0100 MIME-Version: 1.0 Sent to CCL by: "Alexander Kos" [software+/-akosgmbh.eu] The Toxicity database of Symyx is the largest databases with = experimental tox values and structures. You need a license to the database. My = company could provide you with the SDFile. With best regards, Alex AKos Consulting & Solutions Deutschland GmbH (AKos GmbH) Dr. Alexander Kos Austr. 26 D-79585 Steinen Germany Phone: +49 7627 970068 Fax: +49 7627 970067=20 Fax (to mail):=A0=A0 +49 1805 744743 8318 Mobile +49 171 526 9392 E-mail: software..akosgmbh.eu Homepage: www.akosgmbh.de Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, = General Manager: Greta Auf der Maur, Alexander Kos Authorized agent for Symyx Technologies, Inc. (www.symyx.com), DIMENSION = 5, Ltd. (www.miner3d.com), CompuDrug International (www.compudrug.com), Molecular Networks GmbH (www.mol-net.de), and others. -----Original Message----- > From: owner-chemistry+software=3D=3Dakosgmbh.eu..ccl.net [mailto:owner-chemistry+software=3D=3Dakosgmbh.eu..ccl.net] On Behalf Of = richard apodaca rich_apodaca]*[yahoo.com Sent: Montag, 26. Januar 2009 18:32 To: Kos, Alexander J. Subject: CCL: Looking for SDF files for known toxic molecules Sent to CCL by: richard apodaca [rich_apodaca^-^yahoo.com] Gerard, A few are listed here: http://cheminformatics.org/datasets/index.shtml#tox If you compile any new datasets of your own, how would you feel about attaching a license to it that allows free modification and = redistribution? Putting the resulting file(s) under public revision control would be an interesting (and free) way of attracting collaborators around your work: http://depth-first.com/articles/2009/01/23/github-for-chemistry-revision-= con trolled-datasets Just a thought. Rich ___________________________________ Richard L. Apodaca http://depth-first.com Blog http://metamolecular.com Company --- On Mon, 1/26/09, Gerard Pujadas gerard.pujadas#gmail.com wrote: > From: Gerard Pujadas gerard.pujadas#gmail.com > Subject: CCL: Looking for SDF files for known toxic molecules > To: "Apodaca, Rich " > Date: Monday, January 26, 2009, 6:45 AM > Dear CCL list subscribers, >=20 > is there any SDF file of known toxic molecules available > for training a > program that predicts toxicity? >=20 > with many thanks in advances >=20 > yours sincerely >=20 > Gerard -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 16 05:34:01 2009 From: "Uwe Huniar uwe.huniar*cosmologic.de" To: CCL Subject: CCL:G: RI-MP2 fittingbasis set Message-Id: <-38626-090216051429-3064-IOI/R7i+6XsUv1C5c7RWSg^server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Mon, 16 Feb 2009 10:35:04 +0100 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [uwe.huniar###cosmologic.de] Hi, Turbomole uses gaussian basis sets. So the fitting basis sets for RI-MP2 can be used without problems. It might be a good idea to use the Karlsruhe basis sets (TZVP, TZVPP, QZVP,...) together with the fitted auxiliary basis sets instead of 6-311G*. But the TZVP-like auxiliary basis set should be large enough for 6-311G*. Dunning basis sets (cc-pVXZ) and their fitted auxiliary basis set from Turbomole is a good alternative either. But of course only for the elements where Dunning basis sets are available. I have doubts about LANL2DZ for MP2, I guess that this is a far too small basis set to get a reasonable amount of the correlation energy. Same is true for all other double zeta basis sets. Regards, Uwe > I want to use NWChem RI-MP2 for organometallic cluster geometry > optimisation+frequency calculation (in comparison with some DFT > functionals), since my structures depend heavily on weak > interactions. However (unless one uses Turbomole based programs), the > fitting basis sets are very limited (not only in NWChem). I would > need something that goes up to Xe, hence transition metals involved. > I am using gaussian basis sets, such as 6-311G* in combination with > pseudopotentials, such as LANL2DZ. I never quite found a good fitting > basis set for RI-MP2 anywhere for these basis sets. Of course, I > could download those from Turbomole website, but aren't those > "optimized" for slater basis sets? > > What is a good fitting basis set, for that matter? If I found any in > the literature, how can I test with my method and primary basis set > to evaluate if it's "good" fit? Howdo I define or quantify this > goodness of fit? > > thanks > > Jonas Baltrusaitis University of Iowa > > > > -= This is automatically added to each message by the mailing script > =- To recover the email address of the author of the message, please > change the strange characters on the top line to the _+_ sign. You can > alsohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > -- ------------------------------------------------------------------------------ Dr. Uwe Huniar COSMOlogic GmbH&Co.KG Burscheider Str. 515 D-51381 Leverkusen Germany Tel. +49 - 2171 - 36 36 65 Fax +49 - 2171 - 73 16 89 EMail: uwe.huniar_+_cosmologic.de turbomole_+_cosmologic.de info_+_turbomole.com From owner-chemistry@ccl.net Mon Feb 16 06:09:01 2009 From: "Alexander Kos software-#-akosgmbh.eu" To: CCL Subject: CCL:G: Energy level plots Message-Id: <-38627-090215111248-8766-MALuV7h3CRcpMuzwf6Iv7g*server.ccl.net> X-Original-From: "Alexander Kos" Content-Language: de Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Sun, 15 Feb 2009 17:12:35 +0100 MIME-Version: 1.0 Sent to CCL by: "Alexander Kos" [software..akosgmbh.eu] If you manage to get the data into Excel use miner3d (www.miner3d.com) = to do the plotting. With best regards, Alex AKos Consulting & Solutions Deutschland GmbH (AKos GmbH) Dr. Alexander Kos Austr. 26 D-79585 Steinen Germany Phone: +49 7627 970068 Fax: +49 7627 970067=20 Fax (to mail):=A0=A0 +49 1805 744743 8318 Mobile +49 171 526 9392 E-mail: software _ akosgmbh.eu Homepage: www.akosgmbh.de Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, = General Manager: Greta Auf der Maur, Alexander Kos Authorized agent for Symyx Technologies, Inc. (www.symyx.com), DIMENSION = 5, Ltd. (www.miner3d.com), CompuDrug International (www.compudrug.com), Molecular Networks GmbH (www.mol-net.de), and others. -----Original Message----- > From: owner-chemistry+software=3D=3Dakosgmbh.eu _ ccl.net [mailto:owner-chemistry+software=3D=3Dakosgmbh.eu _ ccl.net] On Behalf Of = Adam Tenderholt atenderholt ~~ gmail.com Sent: Freitag, 30. Januar 2009 23:00 To: Kos, Alexander J. Subject: CCL:G: Energy level plots Sent to CCL by: Adam Tenderholt [atenderholt- -gmail.com] Hi Ismael, The cclib package (http://cclib.sf.net) provides a Python library for parsing files from Gaussian and Gamess. With this, you could probably whip together a script to do what you want. For instance, you could create a python script (untested) that writes the MO number and alpha energy level: ---- import sys > from cclib.parser import ccopen logfile =3D ccopen(sys.argv[1]) data =3D logfile.parse() output =3D file.open("energies.dat", "w") for i in range(len(data.moenergies[0])): output.write("%3i %9.3f\n" % (i, data.moenergies[0][i])) output.close() ---- You could open this file up in something like excel and figure out a way to plot the energy level diagram. Hope that helps, Adam On Fri, Jan 30, 2009 at 11:58 AM, Ismael Ortiz Verano ieortizv###bt.unal.edu.co wrote: > Hi! > > Does someone know a package (preferably free, and preferably on linux) = to > make energy level diagrams from MOPAC, GAUSSIAN, GAMESS output files? > > > Thanks in advance. > > > -- > Ismael Ortiz Verano > Grupo de Qu=EDmica Te=F3rica > Universidad Nacional de Colombia > Tel: (57)(1) 3165000 ext 10608 > -=3Dhis is automatically added to each message by the mailing script =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20Search Messages: http://www.ccl.net/htdig (login: ccl, Password: = search)http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon Feb 16 07:17:00 2009 From: "Khaled el sayed el kelany elkelanystar2008- -yahoo.com" To: CCL Subject: CCL: TD/DFT Message-Id: <-38628-090216070940-28340-zCDan1xZbpqy/AMomwo+pA[]server.ccl.net> X-Original-From: "Khaled el sayed el kelany" Date: Mon, 16 Feb 2009 07:09:36 -0500 Sent to CCL by: "Khaled el sayed el kelany" [elkelanystar2008**yahoo.com] Dear Collagues I will approtiate if you guide me to carry out (TD/DFT) calculations to get the excited state. It will be helpful if you send to me the complete inpt and output of ethylene with any basis set. I have guassian 94 and gamess 98 programs. Thanks My sirs From owner-chemistry@ccl.net Mon Feb 16 08:10:01 2009 From: "Khaled El-Sayed El-Kelany elkelanystar2008(a)yahoo.com" To: CCL Subject: CCL:G: TD/DFT calculations Message-Id: <-38629-090216080819-25788-FHpsR4v0q2sqBfrv/lIpYw+*+server.ccl.net> X-Original-From: "Khaled El-Sayed El-Kelany" Date: Mon, 16 Feb 2009 08:08:15 -0500 Sent to CCL by: "Khaled El-Sayed El-Kelany" [elkelanystar2008 _ yahoo.com] Dear Collagues I will approtiate if you can guide me to carry out (TD/DFT) calculations to get the excited state. It will be helpful if you send to me the complete input and output of ethylene with basis set 6-31G** or any other basis set. I have Gaussian 94 and Gamess 98 programes. Thanks Khaled El-Kelany El Minia Universty, El Minia - Egypt Email;elkelanystar2008%x%yahoo.com From owner-chemistry@ccl.net Mon Feb 16 09:23:00 2009 From: "Alexander Kos software:_:akosgmbh.eu" To: CCL Subject: CCL: Code for Polymer chain generation Message-Id: <-38630-090215105945-7666-bAryKcaXWvkPKcgDcn2Q5w/./server.ccl.net> X-Original-From: "Alexander Kos" Content-Language: de Content-Type: multipart/alternative; boundary="----=_NextPart_000_00CF_01C98F8E.C1F4E570" Date: Sun, 15 Feb 2009 16:59:25 +0100 MIME-Version: 1.0 Sent to CCL by: "Alexander Kos" [software^akosgmbh.eu] This is a multipart message in MIME format. ------=_NextPart_000_00CF_01C98F8E.C1F4E570 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit I am not quite sure what you want. If it concerns drawing a polymer chain with connection table use Symyx Draw. With best regards, Alex AKos Consulting & Solutions Deutschland GmbH (AKos GmbH) Dr. Alexander Kos Austr. 26 D-79585 Steinen Germany Phone: +49 7627 970068 Fax: +49 7627 970067 Fax (to mail): +49 1805 744743 8318 Mobile +49 171 526 9392 E-mail: software:-:akosgmbh.eu Homepage: www.akosgmbh.de Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, General Manager: Greta Auf der Maur, Alexander Kos Authorized agent for Symyx Technologies, Inc. ( www.symyx.com), DIMENSION 5, Ltd. ( www.miner3d.com), CompuDrug International ( www.compudrug.com), Molecular Networks GmbH ( www.mol-net.de), and others. > From: owner-chemistry+software==akosgmbh.eu:-:ccl.net [mailto:owner-chemistry+software==akosgmbh.eu:-:ccl.net] On Behalf Of Delwar Hossain hossaind2004~~yahoo.com Sent: Samstag, 14. Februar 2009 00:19 To: Kos, Alexander J. Subject: CCL: Code for Polymer chain generation Hi, I am looking for a code or free software which can generate polymer chain. I highly appreciate your help regarding this matter. Thank you in advance. With best regards, Delwar ------=_NextPart_000_00CF_01C98F8E.C1F4E570 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I am not quite sure what you want. If it concerns drawing = a polymer chain with connection table use Symyx = Draw.

 

With best regards,

Alex

 

 

AKos Consulting & Solutions Deutschland = GmbH

(AKos GmbH)
Dr. Alexander Kos
Austr. 26
D-79585 Steinen
Germany

Phone: +49 7627 970068

Fax: +49 7627 970067

Fax (to mail):   +49 1805 744743 8318
Mobile +49 171 526 9392

E-mail: software:-:akosgmbh.eu=
Homepage: www.akosgmbh.de

Registered at Amtsgericht Freiburg HRB 700872, Ust-ID DE253131617, General Manager: Greta Auf der Maur, Alexander = Kos

Authorized agent for Symyx Technologies, Inc. = = (= www.symyx.com= ), DIMENSION 5, Ltd. (www.miner3d.com= ), CompuDrug International (www.compudrug.com<= /a>= ), Molecular Networks GmbH (www.mol-net.de= = ), and others.

 

 

 

From: owner-chemistry+software=3D=3Dakosgmbh.eu:-:ccl.net [mailto:owner-chemistry+software=3D=3Dakosgmbh.eu:-:ccl.net] On Behalf = Of Delwar Hossain hossaind2004~~yahoo.com
Sent: Samstag, 14. Februar 2009 00:19
To: Kos, Alexander J.
Subject: CCL: Code for Polymer chain = generation

 

Hi,

I am looking for a code or free software which = can generate polymer chain. I highly appreciate your help regarding this = matter.

Thank you in advance.

With best regards,

Delwar

 =

------=_NextPart_000_00CF_01C98F8E.C1F4E570-- From owner-chemistry@ccl.net Mon Feb 16 09:57:00 2009 From: "M. A. A. Ibrahim m.ibrahim1982 ~ yahoo.com" To: CCL Subject: CCL:G: Sr2+ - Complex solvation problem Message-Id: <-38631-090216092648-30895-qBz0ys9oMKOkHPBYessrUg_._server.ccl.net> X-Original-From: "M. A. A. Ibrahim" Date: Mon, 16 Feb 2009 09:26:45 -0500 Sent to CCL by: "M. A. A. Ibrahim" [m.ibrahim1982[a]yahoo.com] Dear CCLers I am writing today to enquire about the following failure message: "Maximum number of bonds =12 on atom 1 exceeded" Gaussian give me this error when I ask to study the solvation effect on Sr2+ complex. If I tried the calculation in gas phase, Everything would be going well. In addition, if I changes atom 1 from Sr2+ to Ca2+, it is going well too. So, why Sr2+ ion has this type of problem and how can I overcome this problem? I took forward to hearing from you. Sincerely; M. Ibrahim From owner-chemistry@ccl.net Mon Feb 16 11:03:00 2009 From: "Cherif Farid Matta cherif.matta(!)msvu.ca" To: CCL Subject: CCL: "Atoms in Molecules" Symposium: Canadian Chemical Conference & Exhibit Message-Id: <-38632-090216033304-14065-IFI7Cv0aX7JqBDSKRg7wKw-.-server.ccl.net> X-Original-From: "Cherif Farid Matta" Date: Mon, 16 Feb 2009 03:33:00 -0500 Sent to CCL by: "Cherif Farid Matta" [cherif.matta^_^msvu.ca] Symposium on "Atoms in Molecules" at the 92nd Canadian Chemical Conference & Exhibition (CSC 2009) - Hamilton Ontario (30 May-5 June, 2009). ========================================================================== We are happy to invite you to participate in the Symposium on interpreting chemical computations at the annual national meeting of the Canadian Society for Chemistry, to be held in Hamilton, Ontario (30 May-5 June 2009) This symposium, in honor of Richard Bader, will be conceptual techniques for interpreting chemical computations. While the title is "Atoms in Molecules" the symposium will be significantly broader, including not only QTAIM but also other theories based on the electron density such as "conceptual" or "chemical" DFT, MO theory, valence bond theory, etc. The list of confirmed speakers below shows that breadth (this list is expected to grow): Confirmed Invited Speakers (so far) ==================================== James Anderson, McMaster University, (Canada) Richard Bader, McMaster University, (Canada) Andre Bandrauk, Universite de Sherbrooke, (Canada) Friedrich Biegler-Knig, Fachhochschule Bielefeld, (Germany) Russell Boyd, Dalhousie University, (Canada) Patrick Bultinck, University of Ghent, (Belgium) Morrel Cohen, Rutgers University, (USA) Fernando Cortez Guzman, Universidad Nacional Autonoma de Mexico (UNAM), (Mexico) Frank De Proft, Vrije University Brussel (VUB), (Belgium) Patrick Fowler, University of Sheffield, (UK) Jose Luis Gazquez, University Aut. Metropolitana (UAM), (Mexico) Paul Geerlings, Vrije University Brussel (VUB), (Belgium) Jesus Hernandez-Trujillo, Universidad Nacional Autonoma de Mexico (UNAM), (Mexico) Samantha Jenkins, University West, (Sweden) Erin Johnson, Duke University, (USA) Todd Keith, Semichem Inc. and University of Missouri (USA) Claude Lecomte, Universite Henri Poincare Nancy 1, (France) Creon Levit, NASA-Ames, (USA) Angel Martin-Pendas, Universidad de Oviedo, (Spain) Lou Massa, Hunter College, City University of New York (CUNY), (USA) Junia Melin, Auburn University, (USA) Vince Ortiz, Auburn University, (USA) Robert Parr, University North Carolina, (USA) Andreas Savin, CNRS, (France) Akitomo Tachibana, Kyoto University, (Japan) Nick Werstiuk, McMaster University, (Canada) Krzysztof Wozniak, Warsaw University, (Poland) Our goal is to facilitate a mind-stimulating exchange not only on what the current status of interpreting chemical computations is, but, more importantly, what the major outstanding problems and what the most promising (and least promising) approaches to those problems are. While Hamilton has an airport (20 minutes from the conference venue), it is often *much* cheaper to fly into Toronto (Pearson Airport; 50 minutes away) or Buffalo, New York, U.S.A. (Buffalo-Niagara; 90 minutes away). Shuttles are available to Hamilton from either airport, provided you reserve the shuttle in advance. Car rentals in Buffalo, but not Toronto, are usually quite affordable.) We hope that you will participate in this event. If you are planning to attend, please submit your abstract BEFORE 18 FEBRUARY 2009. If you cannot meet this deadline, you can still participate by sending your abstract by email to both of us (ayers[at]mcmaster.ca, Cherif.Matta[at]dal.ca). Symposium Website: ================ http://www.csc2009.ca/index.cfm/ci_id/5376/3.htm#Atoms_in_Molecules Conference Website: ================ http://www.csc2009.ca/index.cfm/ci_id/5145/la_id/1.htm For registration details: ========================= http://www.csc2009.ca/index.cfm/ci_id/5147/la_id/1.htm We hope to see you in Hamilton, Paul W. Ayers and Cherif F. Matta ---------------------------------------------- Paul W. Ayers Associate Professor Canada Research Chair in Theoretical Chemistry and Chemical Biology Department of Chemistry McMaster University E-mail: ayers_._mcmaster.ca Webite: http://www.chemistry.mcmaster.ca/ayers/ ---------------------------------------------- Cherif F. Matta Assistant Professor Deparment of Chemistry and Physics Mount Saint Vincent and Adjunct Professor Department of Chemistry Dalhousie University E-mail: cherif.matta_._dal.ca Website: http://www.chem.utoronto.ca/~cmatta/ ---------------------------------------------- From owner-chemistry@ccl.net Mon Feb 16 17:40:02 2009 From: "Jennifer Clare Brookes ucapjcb{=}ucl.ac.uk" To: CCL Subject: CCL:G: BOMD and SimAnneal: Gaussian 03 Message-Id: <-38633-090216111910-27775-ziKQv31kp/J0aAD/e5swEg^server.ccl.net> X-Original-From: "Jennifer Clare Brookes" Date: Mon, 16 Feb 2009 11:19:06 -0500 Sent to CCL by: "Jennifer Clare Brookes" [ucapjcb- -ucl.ac.uk] Dear all, I would like to do some high temperature annealed molecular dynamics (as a way to sample conformational space of a single molecule) using the BOMD option in Gaussian 03, and the SimAnneal keyword. I am confused simply on how to construct the necessary keywords in the route card. Has anyone done this type of simulation? and if so please could I see a sample working input file? Any help much appreciated, Best wishes, Jennifer From owner-chemistry@ccl.net Mon Feb 16 18:18:01 2009 From: "Roman D Gorbunov rgorbuno[*]aecom.yu.edu" To: CCL Subject: CCL: Why the Cartesian Force Constants are negative? Message-Id: <-38634-090216181651-20689-rzScLnB16JK1ng4xaeSNwg~!~server.ccl.net> X-Original-From: "Roman D Gorbunov" Date: Mon, 16 Feb 2009 18:16:47 -0500 Sent to CCL by: "Roman D Gorbunov" [rgorbuno-*-aecom.yu.edu] Dear CCL Subscribers, I need to calculate the Hessian matrix in the Cartesian coordinates (or, in other words, the Cartesian force constants). I managed to do that. However, the results is strange. The Cartesian Hessian matrix contains a lot of negative values. The logical explanation of that would be a "bad" (not optimized) geometry of the system. However, I did the full geometry optimization before the normal mode analysis. Moreover, I tried to use "tight" and "verythight" options during the optimization. It does not help. To be more specific. Here is my input file: %NProcShared=4 %Chk=h2o_5.chk %RWF=f1,245MW,f2,245MW,f3,245MW,f4,245MW,f5,245MW,f6,245MW,f7,245MW,f8,245MW,f9,245MW,f10,-1 %mem=2000MB #B3LYP/6-31G* GFINPUT IOP(7/33=1) Opt=(verytight) Freq=HPModes --------------------------- 0 1 o h 1 ho2 h 1 ho3 2 hoh3 ho2 0.950000 ho3 0.950000 hoh3 109.471 The Cartesian force constants can be found in the formated checkpoint file. The formated checkpoint file can be generated in the following way: formchk h2o_5.chk h2o_5.fchk The Cartesian force constants I got a listed bellow: Cartesian Force Constants R N= 45 -1.30352219E-04 -2.93402327E-12 6.47944946E-01 7.07998333E-13 2.13183069E-11 4.52936930E-01 6.51761136E-05 2.12023356E-12 -7.69336887E-13 -7.81771955E-05 1.45637163E-12 -3.23972473E-01 1.86885940E-01 -1.42985366E-12 3.55386162E-01 -1.86028892E-12 2.54765629E-01 -2.26468465E-01 7.31122815E-13 -2.20825784E-01 2.13407140E-01 6.51761126E-05 2.23882420E-12 -1.71315211E-12 1.30010790E-05 -1.00264854E-12 1.89289293E-12 -7.81771955E-05 1.98411541E-12 -3.23972473E-01 -1.86885940E-01 -1.00264640E-12 -3.14136893E-02 -3.39398443E-02 -1.43037292E-12 3.55386162E-01 3.63513055E-12 -2.54765629E-01 -2.26468465E-01 -1.89288905E-12 3.39398443E-02 1.30613251E-02 -7.31477658E-13 2.20825784E-01 2.13407140E-01 Can anybody help me with that problem? Thank you in advance, Roman From owner-chemistry@ccl.net Mon Feb 16 21:34:00 2009 From: "Grant Hill jghill!=!wsu.edu" To: CCL Subject: CCL:G: RI-MP2 fittingbasis set Message-Id: <-38635-090216190520-25083-YPhohhTFJNORjHPuMVSccA _ server.ccl.net> X-Original-From: Grant Hill Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Mon, 16 Feb 2009 15:11:10 -0800 Mime-Version: 1.0 (Apple Message framework v930.3) Sent to CCL by: Grant Hill [jghill(0)wsu.edu] To follow on from Uwe's comments, correlation consistent AO and auxiliary basis sets are available for most of the elements up to Xe, although fitting sets may be missing for those final 5p elements. Assuming that it fits into your research plans I would give some serious thought to switching to either the Karlsruhe or correlation consistent sets for the AO basis, this would mean that you probably wouldn't need to investigate how accurate the fitting is. If changing the AO basis is not an option it would be prudent to benchmark/test the fitting with auxiliary sets by running both DF-MP2 and conventional MP2 calculations, for example, see C. Hattig, Phys. Chem. Chem. Phys. vol 7 (2005), 59-66. Finally, while I'm not up-to-speed on the capabilities of NWChem, it may be worth investigating DF-HF (or RI-HF if you prefer that moniker), depending on application and basis set you may find it produces great reductions in computational cost. One place to start investigating this is by reading F. Weigend, J. Comput. Chem. vol 29 (2008), 167-175 and references therein. Regards, Grant On 16 Feb 2009, at 01:35, Uwe Huniar uwe.huniar*cosmologic.de wrote: > > Sent to CCL by: Uwe Huniar [uwe.huniar###cosmologic.de] > Hi, > > Turbomole uses gaussian basis sets. So the fitting basis sets for RI- > MP2 > can be used without problems. It might be a good idea to use the > Karlsruhe basis sets (TZVP, TZVPP, QZVP,...) together with the fitted > auxiliary basis sets instead of 6-311G*. But the TZVP-like auxiliary > basis set should be large enough for 6-311G*. > > Dunning basis sets (cc-pVXZ) and their fitted auxiliary basis set from > Turbomole is a good alternative either. But of course only for the > elements where Dunning basis sets are available. > > I have doubts about LANL2DZ for MP2, I guess that this is a far too > small basis set to get a reasonable amount of the correlation energy. > Same is true for all other double zeta basis sets. > > Regards, > > Uwe > >> I want to use NWChem RI-MP2 for organometallic cluster geometry >> optimisation+frequency calculation (in comparison with some DFT >> functionals), since my structures depend heavily on weak >> interactions. However (unless one uses Turbomole based programs), the >> fitting basis sets are very limited (not only in NWChem). I would >> need something that goes up to Xe, hence transition metals involved. >> I am using gaussian basis sets, such as 6-311G* in combination with >> pseudopotentials, such as LANL2DZ. I never quite found a good fitting >> basis set for RI-MP2 anywhere for these basis sets. Of course, I >> could download those from Turbomole website, but aren't those >> "optimized" for slater basis sets? >> >> What is a good fitting basis set, for that matter? If I found any in >> the literature, how can I test with my method and primary basis set >> to evaluate if it's "good" fit? Howdo I define or quantify this >> goodness of fit? >> >> thanks >> >> Jonas Baltrusaitis University of Iowa >> >> >> >> -= This is automatically added to each message by the mailing script >> =- To recover the email address of the author of the message, please >> change the strange characters on the top line to the ,+, sign. You >> can >> alsohttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: >> http://server.ccl.net/chemistry/announcements/conferences/ >> >> Search Messages: http://www.ccl.net/htdig (login: ccl, Password: >> search)> >> >> >> > > -- > ------------------------------------------------------------------------------ > Dr. Uwe Huniar > COSMOlogic GmbH&Co.KG > Burscheider Str. 515 > D-51381 Leverkusen > Germany > Tel. +49 - 2171 - 36 36 65 > Fax +49 - 2171 - 73 16 89 > EMail: uwe.huniar,+,cosmologic.de > turbomole,+,cosmologic.de > info,+,turbomole.com > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> >