From owner-chemistry@ccl.net Thu Apr 29 00:37:01 2010 From: "Venable, Richard (NIH/NHLBI) E venabler#,#nhlbi.nih.gov" To: CCL Subject: CCL: Bulding a Chemical database Message-Id: <-41730-100428213404-24152-qHW0w21DN6Ce71lc+xnEkw%%server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 28 Apr 2010 20:57:12 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler::nhlbi.nih.gov] If your search includes commercial products that might be easier to use tha= n Access, I suggest you also consider FileMaker Pro (www.filemaker.com). I= t runs on both Windows and Mac OS X, and has a Container field which can be= used to store document files, graphics objects, and much more. It can imp= ort from Excel, and has data exchange capabilities with a number of SQL com= pliant packages. I don't know anyone at the company, or have any stock, etc.; I've just used= the package myself for a few trivial things, and seen other people do some= fairly impressive things with it in a scientific laboratory setting. -- Rick Venable Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. On 4/28/10 5:24 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: Sent to CCL by: Adam Tenderholt [atenderholt,gmail.com] I can think of a couple of factors that you should probably mention or be thinking about before deciding on which software to go with. -Will the database be edited by multiple people? How many people will be accessing the database (read-only)? -Does the database need to be functioning ASAP or do you have time to look for a more elegant solution? -Do you want versioning or a history of changes made to the database? I think there's also an open source project to build a database platform similar to what you're after, but I can't remember its name. Maybe look on sites like sourceforge.net and freshmeat.net? Adam On Wed, Apr 28, 2010 at 1055 AM, Ronald L Cook cookrl%a%tda.com wrote: > > Sent to CCL by: "Ronald L Cook" [cookrl() tda.com] > Hi All > > We are carrying out a comprehensive computational study of a series of mo= lecules including optimization and property calculations at the RB3LYP 6-31= 1++F(d,p) level to generate QM descriptors. We are also calculating MEP ma= ps, charges on atoms, and Fukui indices using Hirshfeld population analysis= . We would also like to store graphics of the the optimized structures. > > When we started out we were using Excel to store and probe the results. = This has gotten quite unwieldly. Does anyone have any recommendations for = the best database software (e.q. Access or software more directed to chemis= ts)? Or can anyone recommend a good book on building a chemical database f= rom Access or the various forms of SQL software. > > Thanks in Advance for your advise > > Ronald Cook > Principal Scientist > TDA research, Inc. From owner-chemistry@ccl.net Thu Apr 29 05:25:00 2010 From: "Arvydas Tamulis tamulis]^[itpa.lt" To: CCL Subject: CCL: Isotropic Fermi contact couplings in excited states Message-Id: <-41731-100429041039-15438-yrntrnPzbGvwmBwj34pxVA..server.ccl.net> X-Original-From: Arvydas Tamulis Content-Type: TEXT/PLAIN; format=flowed; charset=US-ASCII Date: Thu, 29 Apr 2010 10:32:19 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Arvydas Tamulis [tamulis|a|itpa.lt] Dear Colleagues, Which program package calculate electron spin density together with Isotropic Fermi contact couplings in various electronic excited states? With best regards, Arvydas Tamulis http://www.itpa.lt/~tamulis/ From owner-chemistry@ccl.net Thu Apr 29 07:10:00 2010 From: "Joe Leonard jleonard42/a\gmail.com" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41732-100429070801-9092-jwvEbD6l3T/tDrEyjlHlaA|*|server.ccl.net> X-Original-From: Joe Leonard Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Thu, 29 Apr 2010 07:07:23 -0400 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: Joe Leonard [jleonard42|gmail.com] Folks, Has anybody successfully used remote desktop software from a Mac (Snow = Leopard) to a headless PC (Windows XP or 7), especially for running 3D = graphics such as PyMOL? While I am a mac-o-phile, there are various = programs that aren't available that I am interested in. There are also = a lot of interesting little machines appearing (Nvidia ION desktops, = etc). If I could have the machine and not have to worry about KVM = switching, that would be a win. What software did you use, and did it work over WIFi or was a cable = connection required? Inquiring minds want to know! Thanks in advance! Joe Leonard jleonard42++gmail.com -- Is the question "Where do babies come from?" really a science question? = Yes. Geography to be specific. Croydon to be precise. From owner-chemistry@ccl.net Thu Apr 29 08:40:01 2010 From: "Daniel Jana dfjana%%gmail.com" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41733-100429083643-21842-HQyK4GEczfKa1k8lnUtAlQ+*+server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 29 Apr 2010 14:36:33 +0200 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana.{:}.gmail.com] Hello, A fast search in google revealed this: http://www.microsoft.com/mac/products/remote-desktop/default.mspx Considering the source, should be your best bet. Wifi should be enough, as long as we're talking about all computers in the same (local) network. Best of luck, Daniel On 29 April 2010 13:07, Joe Leonard jleonard42/agmail.com wrote: > > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] > Folks, > > Has anybody successfully used remote desktop software from a Mac (Snow Le= opard) to a headless PC (Windows XP or 7), especially for running 3D graphi= cs such as PyMOL? =A0While I am a mac-o-phile, there are various programs t= hat aren't available that I am interested in. =A0There are also a lot of in= teresting little machines appearing (Nvidia ION desktops, etc). =A0If I cou= ld have the machine and not have to worry about KVM switching, that would b= e a win. > > What software did you use, and did it work over WIFi or was a cable conne= ction required? =A0Inquiring minds want to know! > > Thanks in advance! > > Joe Leonard > jleonard42[]gmail.com > -- > Is the question "Where do babies come from?" really a science question? = =A0Yes. Geography to be specific. Croydon to be precise. > > > > - This is automatically added to each message by the mailing script -> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Apr 29 09:14:01 2010 From: "Walker Ross rcw[*]sdsc.edu" To: CCL Subject: CCL:G: Linux vs Windows Message-Id: <-41734-100429030002-3479-3dj57W49Xcm0YkNL5nxHag .. server.ccl.net> X-Original-From: "Walker Ross" Content-Language: en-us Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 28 Apr 2010 23:59:53 -0700 MIME-Version: 1.0 Sent to CCL by: "Walker Ross" [rcw%x%sdsc.edu] Dear Andr=E1s > 1) I have no experience with comparison of Gaussian at Windows and > Linux, > but I have never seen (in the last 15 years) any computation-intensive > application which runs at Windows better. This is not true. We recently completed a port of AMBER's PMEMD = molecular dynamics engine to Windows HPC server, it runs on Windows XP, Vista, 7 = as well and it typically runs between 5% and 20% faster than on standard = Linux clusters (RHEL4). The difference in serial is minimal but in parallel performance is typically better in a large part due to the efficiency of msmpi compared with MVAPICH and mpich2 which we typically use. With regards to Gaussian on Windows I have not tried 2009 but the big problem with G03W was always that it only runs on a single core and in = this day and age of multicore machines that isn't very helpful so it doesn't really matter how it compares with the single core Linux version. This = may have been addressed in G09W, I do not know. All the best Ross /\ \/ |\oss Walker | Assistant Research Professor | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross^rosswalker.co.uk |=20 | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ | Note: Electronic Mail is not secure, has no guarantee of delivery, may = not be read every day, and should not be used for urgent or sensitive = issues. =20 =20 From owner-chemistry@ccl.net Thu Apr 29 09:50:01 2010 From: "=?GB2312?B?0vO9oQ==?= janeyin600_._gmail.com" To: CCL Subject: CCL:G: MP2 failure Message-Id: <-41735-100429025838-31642-q+o8NKv53paIVUQr6L9F/g]_[server.ccl.net> X-Original-From: =?GB2312?B?0vO9oQ==?= Content-Type: multipart/alternative; boundary=00032555623a76c945048559c0ab Date: Thu, 29 Apr 2010 00:53:54 -0500 MIME-Version: 1.0 Sent to CCL by: =?GB2312?B?0vO9oQ==?= [janeyin600|-|gmail.com] --00032555623a76c945048559c0ab Content-Type: text/plain; charset=ISO-8859-1 Hi there, I have some trouble with calculating some MP2 jobs recently. I found that the combination of "opt freq" will automatically generate a link after the energy has converged: Normal termination of Gaussian 03 at Wed Apr 28 06:22:56 2010. Link1: Proceeding to internal job step number 2. -------------------------------------------------------------------- #N Geom=AllCheck Guess=Read SCRF=Check GenChk UMP2(FC)/6-31G(d) Freq and then it will continue to run for a while. For most MP2 jobs I am now carrying on, it finished the first step, but failed at the second step. I am now separating "freq" and "opt" commands. Don't know if that works... Any advice? Thank you very much~~ Jane --00032555623a76c945048559c0ab Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi there,
=A0
I have some trouble wi= th calculating=A0some MP2=A0jobs recently. I=A0found that=A0the combination= of "opt=A0freq" will=A0automatically generate=A0a link after the= energy has converged:
=A0
=A0Normal terminat= ion of Gaussian 03 at Wed Apr 28 06:22:56 2010.
=A0Link1:=A0 Proceeding = to internal job step number=A0 2.
=A0--------------------------------------------------------------------
= =A0#N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk UMP2(FC)/6-31G(d) Fr= eq
and then it will= continue to run for a while. For most=A0MP2 jobs I am now carrying on, it = finished the first step, but failed at the second step. I am now separating= "freq" and "opt" commands. Don't know if that work= s...
=A0
Any advice? Thank you very= much~~
=A0
Jane
--00032555623a76c945048559c0ab-- From owner-chemistry@ccl.net Thu Apr 29 10:25:00 2010 From: "Uwe Huniar huniar[A]cosmologic.de" To: CCL Subject: CCL:G: B3LYP and def2-TZVP Message-Id: <-41736-100429053824-29034-4FMTU538Fn6zfcXyHph0OA#server.ccl.net> X-Original-From: Uwe Huniar Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Thu, 29 Apr 2010 10:59:26 +0200 MIME-Version: 1.0 Sent to CCL by: Uwe Huniar [huniar..cosmologic.de] Hi John, partially correct. def2-TZVP is identical to def-TZVPP for some elements, but not for all. So generally it is not the same to use def-TZVPP or def2-TZVP. The problem with the Turbomole (or Ahlrichs or Karlsruhe) basis sets is often, that people get confused with the names. What is def- or def2- standing for? Is TZVP the same as def-TZVP, and what about DZP, TZP, etc... I will try to answer some of the questions below. Anyone who is not interested in those basis sets can stop reading here. Alfredo: at the end of this post there is a link to the Turbomole basis set library download site. If you do not find def2-TZVP at PNL basis set library, you can download the basis set in different formats from the link given below. --- First, just forget about the old TZP, DZP, etc. basis sets (those which do not contain a V for valence in the name) which have been published before 1990, they are hardly used any more. SVP stems from 1992, TZVP from 1994, QZVP from 2003 (references and details see below the link to the Turbomole basis set library website, there click on the big green [Readme] button). To avoid confusion with the previously published basis sets with similar names, the Ahlrichs group called them def- which stands for 'default' about 15 years ago. So def-SV(P), def-TZVP, def-QZVP, etc. are the basis sets which have been used as default in Turbomole. Nowadays we recommend to use def2- instead of def- for reasons described below. Perhaps those few lines from the Turbomole documentation can help to get an overview: - def-SV(P) for routine SCF or DFT. Quality is about 6–31G*. - def-TZVP for accurate SCF or DFT. Quality is slightly better than 6–311G**. - def-TZVPP for MP2 or close to basis set limit SCF or DFT. Comparable to 6–311G(2df). - def-QZVP and def-QZVPP for highly correlated treatments; quadruple zeta + 3d2f1g or 4d2f1g (beyond Ne), 3p2d1f for H. With the quadruple zeta basis sets from 2003 Weigend et al. have tested the accuracy of def-SVP and def-TZVP in comparison to def-QZVP. It turned out that for many elements the accuracy of TZVP and SVP basis sets have not been consistent, partly just additional polarization functions have been missing (this is what John was referring to). In 2005 the paper with the new def2- basis sets have been published: "These basis sets are designed to give similar errors all accross the periodic table for a given basis set type." (F. Weigend, basis set download site). For organic molecules and properties like energy or structures the difference is not really noticeable. For heavier elements or properties like NMR chemical shieldings def2-TZVP is highly recommended. Here the promised link: http://bases.turbo-forum.com/TURBOMOLE_BASISSET_LIBRARY/tbl.html Supported formats: Turbomole, Gaussian, Dalton, Molpro Sorry for the lengthy post on CCL! Regards, Uwe Am 28.04.2010 21:57, schrieb John McKelvey jmmckel^^^gmail.com: > > Sent to CCL by: John McKelvey [jmmckel++gmail.com] > Partial answer: In the TURBOMOLE basis set directory it is pointed > out that def2-TZVP basis is the same as TZVPP. If that is not > available in Gaussian it might be possible to get it from the PNL web > site. > > John McKelvey > > On Wed, Apr 28, 2010 at 2:07 PM, Alfredo Tlahuice tlahuicef() > yahoo.com wrote: >> >> Sent to CCL by: "Alfredo Tlahuice" [tlahuicef===yahoo.com] >> Hi there >> I want to start a gaussian 03 calculation using the def2-TZVP basis. >> So my question is how can I define that basis set in G03? >> >> Thanks in advance.> >> >> > > > -- ------------------------------------------------------------------------------ Dr. Uwe Huniar COSMOlogic GmbH & Co. KG From owner-chemistry@ccl.net Thu Apr 29 11:00:00 2010 From: "Iain Moal Iain.Moal^cancer.org.uk" To: CCL Subject: CCL: How i do to model a protein which sequence no have a homologue in PDB? Message-Id: <-41737-100429063824-13459-PR+LoZnni2L0XKMas5obxg(a)server.ccl.net> X-Original-From: "Iain Moal" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01CAE788.114FF289" Date: Thu, 29 Apr 2010 11:38:12 +0100 MIME-Version: 1.0 Sent to CCL by: "Iain Moal" [Iain.Moal^-^cancer.org.uk] This is a multi-part message in MIME format. ------_=_NextPart_001_01CAE788.114FF289 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable With difficulty. Perhaps the protein is intrinsically disordered (the Dis= oPred2 server may help you find this out). If so, then you can forget abo= ut getting a homology model because there is no native structures. If not= , you might be able to get a near-native from I-TASSER or Robetta, two of = the best ab initio folding methods. I-TASSER predicts the accuracy of you= r model. If this isn't below a few angstroms or so, then you won't be abl= e to dock the structure and get meaningful results. Usually, the docking = of ab initio structures is beyond current capabilities, unless the protein= is either very small or the binding enthalpy is very low, and even then, = an accurate model is need in the first place. Sent to CCL by: "Carlos Alberto Ortega" [caoz96:yahoo.es] How i do to model a protein which sequence no have a homologue in PDB? The complete sequence no have a homologue in PDB, only have a homologue fo= r a part of the sequenece, and the rest no have homologues. I take the structure which is homologue a seccion of the sequence and try = to model in server webs, but the protein model is not very well for my jud= gment. I use the server I-TASSER server, swissmodel, MODELLER and i try to= use the FUGUE in Sybyl, but how i known which is the best model? and can = i use this model for docking? Thanks very much for your help. -=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=20http://www.ccl.net/spammers.txtThis communication is from Cancer Research UK. Our website is at www.cance= rresearchuk.org. We are a charity registered under number 1089464 and a co= mpany limited by guarantee registered in England & Wales under number 4325= 234. Our registered address is 61 Lincoln's Inn Fields, London WC2A 3PX. O= ur central telephone number is 020 7242 0200. =20 This communication and any attachments contain information which is confid= ential and may also be privileged. It is for the exclusive use of the in= tended recipient(s). If you are not the intended recipient(s) please note= that any form of disclosure, distribution, copying or use of this communi= cation or the information in it or in any attachments is strictly prohibit= ed and may be unlawful. If you have received this communication in error,= please notify the sender and delete the email and destroy any copies of i= t. =20 E-mail communications cannot be guaranteed to be secure or error free, as = information could be intercepted, corrupted, amended, lost, destroyed, arr= ive late or incomplete, or contain viruses. We do not accept liability fo= r any such matters or their consequences. Anyone who communicates with us= by e-mail is taken to accept the risks in doing so. ------_=_NextPart_001_01CAE788.114FF289-- From owner-chemistry@ccl.net Thu Apr 29 11:34:00 2010 From: "Jos P. Cer n-Carrasco jpceron-,-um.es" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41738-100429084149-30704-gccLWVHxExQ0RrOUIeEBBw=server.ccl.net> X-Original-From: "Jos P. Cer n-Carrasco" Date: Thu, 29 Apr 2010 08:41:47 -0400 Sent to CCL by: "Jos P. Cer n-Carrasco" [jpceron%x%um.es] I've used 'Remote Desktop Connection Client for Mac 2' without any problem (from Mac OS X 10.6.3 to WinXP). This is the link to free download: http://www.microsoft.com/mac/products/remote-desktop/default.mspx You can also try with virtual machines, like VMWare Fusion ($) or VirtualBox (free). Hope this helps! Jos P. Cern-Carrasco From owner-chemistry@ccl.net Thu Apr 29 12:09:00 2010 From: "Toomas Tamm tt-ccl2_+_yki.ttu.ee" To: CCL Subject: CCL:G: B3LYP and def2-TZVP Message-Id: <-41739-100429053434-16110-azeqOzV7TzBnxumDlm5wGA . server.ccl.net> X-Original-From: Toomas Tamm Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Thu, 29 Apr 2010 11:32:46 +0300 Mime-Version: 1.0 Sent to CCL by: Toomas Tamm [tt-ccl2*o*yki.ttu.ee] On Wed, 2010-04-28 at 15:57 -0400, John McKelvey jmmckel^^^gmail.com wrote: > Sent to CCL by: John McKelvey [jmmckel++gmail.com] > Partial answer: In the TURBOMOLE basis set directory it is pointed > out that def2-TZVP basis is the same as TZVPP. If that is not > available in Gaussian it might be possible to get it from the PNL web > site. According to the paper which introduces the "def2" basis sets (Weigend and Ahlrichs, PCCP 2005, 7, 3297) the "def" and "def2" basis sets for light elements are not in one-to-one correspondence. For example, the "def2-TZVP" for hydrogen is the same as "def-TZVP", while for carbon, the "def2-TZVP" corresponds to "def-TZVPP". For consistent and correct results, I would recommend downloading the basis sets from the PNL site (https://bse.pnl.gov/bse/portal) and using the GEN keyword in Gaussian to input them directly. Toomas Tamm From owner-chemistry@ccl.net Thu Apr 29 12:45:01 2010 From: "xunlei ding dingxunlei,gmail.com" To: CCL Subject: CCL:G: MP2 failure Message-Id: <-41740-100429105452-30722-/ZZR8PJ1rFaatSBWR74oTA(_)server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Date: Thu, 29 Apr 2010 22:54:42 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei]^[gmail.com] HI, Opt and freq are two jobs. You can run them together with one input file. And also you can run them one by one. In the freq job be sure to use the optimized structure from the previous opt job. Ding =D4=DA 2010=C4=EA4=D4=C229=C8=D5 =CF=C2=CE=E71:53=A3=AC=D2=F3=BD=A1 janeyin= 600_._gmail.com =D0=B4=B5=C0=A3=BA > Hi there, > > I have some trouble with calculating some MP2 jobs recently. I found > that the combination of "opt freq" will automatically generate a link aft= er > the energy has converged: > > Normal termination of Gaussian 03 at Wed Apr 28 06:22:56 2010. > Link1: Proceeding to internal job step number 2. > -------------------------------------------------------------------- > #N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk UMP2(FC)/6-31G(d) Fr= eq > and then it will continue to run for a while. For most MP2 jobs I am now > carrying on, it finished the first step, but failed at the second step. I= am > now separating "freq" and "opt" commands. Don't know if that works... > > Any advice? Thank you very much~~ > > Jane --=20 ------------------------------------------------------ Xun-Lei Ding (=B6=A1=D1=B8=C0=D7) Associate Research Professor of Physical Chemistry, Ph.D State Key Lab for Struct. Chem. of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2=A3=AC Beijing 100190, P. R. China Phone 86-10-62568330 Fax 86-10-62559373 From owner-chemistry@ccl.net Thu Apr 29 13:19:00 2010 From: "Daniel Cappel daniel.cappel\a/schrodinger.com" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41741-100429092844-15679-d3nIV0Yg22fYFJjKtrB6kw*server.ccl.net> X-Original-From: Daniel Cappel Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 29 Apr 2010 14:28:37 +0200 MIME-Version: 1.0 Sent to CCL by: Daniel Cappel [daniel.cappel]_[schrodinger.com] Hi Joe, did you know, that PyMOL is also available for Mac. Just take a look at: http://www.pymol.org/ Best regards, Daniel Cappel On Thu, Apr 29, 2010 at 1:07 PM, Joe Leonard jleonard42/agmail.com wrote: > > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] > Folks, > > Has anybody successfully used remote desktop software from a Mac (Snow Le= opard) to a headless PC (Windows XP or 7), especially for running 3D graphi= cs such as PyMOL? =A0While I am a mac-o-phile, there are various programs t= hat aren't available that I am interested in. =A0There are also a lot of in= teresting little machines appearing (Nvidia ION desktops, etc). =A0If I cou= ld have the machine and not have to worry about KVM switching, that would b= e a win. > > What software did you use, and did it work over WIFi or was a cable conne= ction required? =A0Inquiring minds want to know! > > Thanks in advance! > > Joe Leonard > jleonard42[]gmail.com --=20 Daniel Cappel - Schr=F6dinger - Applications Scientist http://www.schrodinger.com ---------------------------------------------------------------- Sitz der Gesellschaft/Registered Office: Schr=F6dinger GmbH, Dynamostr. 13, D-68165 Mannheim Gesch=E4ftsf=FChrer/Managing Director: Dr. J=F6rg Weiser Handelsregister/Commercial Register: HRB 9583 Amtsgericht Mannheim From owner-chemistry@ccl.net Thu Apr 29 13:54:00 2010 From: "Pablo Vitoria pablo.vitoria,,ehu.es" To: CCL Subject: CCL:G: B3LYP and def2-TZVP Message-Id: <-41742-100429073718-27494-cJ33iu7WORPfWEq0nbDjDQ[-]server.ccl.net> X-Original-From: Pablo Vitoria Content-Type: multipart/mixed; boundary="------------000702020806030306010104" Date: Thu, 29 Apr 2010 13:06:26 +0200 MIME-Version: 1.0 Sent to CCL by: Pablo Vitoria [pablo.vitoria---ehu.es] This is a multi-part message in MIME format. --------------000702020806030306010104 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Hi, In fact those basis sets are available in Gaussian format from the Turbomole site here: http://bases.turbo-forum.com/TURBOMOLE_BASISSET_LIBRARY/tbl.html Cheers Pablo John McKelvey jmmckel^^^gmail.com escribió: > Sent to CCL by: John McKelvey [jmmckel++gmail.com] > Partial answer: In the TURBOMOLE basis set directory it is pointed > out that def2-TZVP basis is the same as TZVPP. If that is not > available in Gaussian it might be possible to get it from the PNL web > site. > > John McKelvey > > On Wed, Apr 28, 2010 at 2:07 PM, Alfredo Tlahuice tlahuicef() > yahoo.com wrote: > >> Sent to CCL by: "Alfredo Tlahuice" [tlahuicef===yahoo.com] >> Hi there >> I want to start a gaussian 03 calculation using the def2-TZVP basis. >> So my question is how can I define that basis set in G03? >> >> Thanks in advance.> >> >> >> > > > > -- ******************************** Pablo Vitoria Garcia Servicios Generales de Rayos X Universidad del País Vasco (UPV/EHU) Fac. Ciencia y Tecnología, Edificio CD4 c/ Barrio Sarriena s/n, 48940 Leioa (Bizkaia) Web: http://www.ehu.es/SGIker/es/rayos_x Tfno. +34 946015334 Fax +34 946013500 ******************************** --------------000702020806030306010104 Content-Type: text/x-vcard; charset=utf-8; name="pablo_vitoria.vcf" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="pablo_vitoria.vcf" begin:vcard fn;quoted-printable:Pablo Vitoria Garc=C3=ADa n;quoted-printable:Vitoria Garc=C3=ADa;Pablo org;quoted-printable:Universidad del Pa=C3=ADs Vasco (UPV/EHU);Servicios Generales de Rayos X adr;quoted-printable;quoted-printable:Barrio Sarriena s/n;;Facultad de Ciencia y Tecnolog=C3=ADa, despacho CD4.S1.6;Leioa;Bizkaia;E-48940;Espa=C3=B1a email;internet:pablo.vitoria.[-].ehu.es title;quoted-printable:T=C3=A9cnico SGIKer tel;work:946015334 tel;fax:946013500 tel;cell:660959834 url:http://www.ehu.es/SGIker/es/rayos_x version:2.1 end:vcard --------------000702020806030306010104-- From owner-chemistry@ccl.net Thu Apr 29 14:29:00 2010 From: "Vincent Leroux vincent.leroux*_*loria.fr" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41743-100429093644-23556-B9IqUzRrEs1IkdhyOR9K/A|-|server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 29 Apr 2010 15:36:33 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux%%loria.fr] Hi, The bandwitch to transmit a video signal at the resolution of a computer screen in real-time is far too high, so you can forget free remote control software like TeamViewer - those are only great to fix relatives' computers from a distance. You usually get something like 1-5 fps of (highly compressed/degraded) video signal transmitted on a broadband connexion... I would suggest you to try virtualization software, provided your Mac has enough memory (ideally 4 GB, but 2 GB is fine). VirtualBox from Sun is free, stable and has good performance. It is working well for running all those useful tools not available on the Mac, such as chemical 2D drawing programs, XnView (Windows), XFig, XmGrace (Linux)... Even dinosaurs like InsightII that do not even work on modern Linux distributions can be revived without using a dedicated computer. On the Mac Parallels Desktop has superior 3D performance, but you need to pay for it (plus pay again for each major update) and it is Mac-only so the hard disk images are not portable outside the Apple world. Therefore VirtualBox has a big advantage, especially when colleagues (some of which might not be Mac fanatics ;-) ) are interested: created guest images (that can contain various versions of Windows and Linux) can be easily transferred from/to Mac/Linux/Windows computers. Regards, VL Le 29/04/10 13:07, Joe Leonard jleonard42/agmail.com a écrit : > > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] > Folks, > > Has anybody successfully used remote desktop software from a Mac (Snow Leopard) to a headless PC (Windows XP or 7), especially for running 3D graphics such as PyMOL? While I am a mac-o-phile, there are various programs that aren't available that I am interested in. There are also a lot of interesting little machines appearing (Nvidia ION desktops, etc). If I could have the machine and not have to worry about KVM switching, that would be a win. > > What software did you use, and did it work over WIFi or was a cable connection required? Inquiring minds want to know! > > Thanks in advance! > > Joe Leonard > jleonard42[]gmail.com > -- > Is the question "Where do babies come from?" really a science question? Yes. Geography to be specific. Croydon to be precise. > > > > -=his is automatically added to each message by the mailing script =-> > > From owner-chemistry@ccl.net Thu Apr 29 15:04:01 2010 From: "David Watson dewatson^olemiss.edu" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41744-100429092412-11341-DyiHOilYJtP9O8G4iPIz+Q|a|server.ccl.net> X-Original-From: David Watson Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Thu, 29 Apr 2010 07:52:51 -0500 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: David Watson [dewatson,+,olemiss.edu] On Apr 29, 2010, at 6:07 AM, Joe Leonard jleonard42/agmail.com wrote: >=20 > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] > Folks, >=20 > Has anybody successfully used remote desktop software from a Mac (Snow = Leopard) to a headless PC (Windows XP or 7), especially for running 3D = graphics such as PyMOL? While I am a mac-o-phile, there are various = programs that aren't available that I am interested in. There are also = a lot of interesting little machines appearing (Nvidia ION desktops, = etc). If I could have the machine and not have to worry about KVM = switching, that would be a win. >=20 I don't understand why you would want to run PyMOL remotely as there is = a perfectly fine implementation for Mac OS X already available from = exactly the same source. As to the matter of running programs remotely on a headless PC, I have = found much success with the free "Remote Desktop Connection" software = available from Microsoft. RDC runs fairly smoothly, and you can customize the graphics for = full-screen usage if you wish. Another alternative is to use LogMeIn from logmein.com, although you may = need to navigate around for a while to locate the free version. This option requires that you install software on both the "server" and = the "client", so that may or may not be an acceptable solution to you. Both of these options are going to be a little clunky if you are trying = to visualize and display complex macromolecules in "ball & stick" or = "surface" modes, as there will be quite a lot of graphical information = being updated if you wish to translate or rotate the molecule. It's sort of the same story if you use XQuartz and X11 windowing to a = remote Linux or Unix server. > What software did you use, and did it work over WIFi or was a cable = connection required? Inquiring minds want to know! >=20 You won't be able to do modeling without a high speed connection. Gigabit ethernet is the way to go, unless by some magical chance you = have a fiber network card in your mac and a fiber switch in your lab. Of course you can remotely log-in over wireless, but I think you will = soon tire of the time it takes to get any work accomplished. From owner-chemistry@ccl.net Thu Apr 29 15:39:00 2010 From: "David Hall drhall- -bu.edu" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41745-100429092742-14655-c5Z40KlQz1StAHXubqT1RA .. server.ccl.net> X-Original-From: David Hall Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Thu, 29 Apr 2010 08:55:37 -0400 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: David Hall [drhall++bu.edu] On Apr 29, 2010, at 7:07 AM, Joe Leonard jleonard42/agmail.com wrote: > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] >=20 > Has anybody successfully used remote desktop software from a Mac (Snow = Leopard) to a headless PC (Windows XP or 7), especially for running 3D = graphics such as PyMOL? =20 Not answering your question, but you can run PyMOL on Mac. For a long = time, PyMOL performance was even a benchmark on Apple's web site for = their high-end machines. You can install PyMOL using either fink ( = http://pdb.finkproject.org/pdb/package.php/pymol-py26 ) or macports ( = http://trac.macports.org/browser/trunk/dports/science/pymol/Portfile ). = Both of these require you to have Apple's Developer Tools installed so = you have a compiler, available for free from either your OS installation = disc or as a download from Apple's site ( = http://developer.apple.com/technologies/xcode.html , download requires = registration ). Also, depending on your version of OS X, you may or may = not already have X11 installed. For Leopard, it's probably a good idea = to get the latest version from http://xquartz.macosforge.org/trac/wiki , = but for Snow Leopard, the one that ships with the OS should be fine. I'd be happy to be proven wrong, but the performance of running any 3D = graphics on your computer will greatly outperform remote desktop = solutions. My past experience with both VNC and Remote Desktop hasn't = been great. -David= From owner-chemistry@ccl.net Thu Apr 29 16:15:01 2010 From: "Alfredo Tlahuice tlahuicef!=!yahoo.com" To: CCL Subject: CCL: ISSPIC XV abstracts submissions Message-Id: <-41746-100429124038-4125-hh3gn/LHy+CWPgOMlQZSHw-$-server.ccl.net> X-Original-From: "Alfredo Tlahuice" Date: Thu, 29 Apr 2010 12:40:36 -0400 Sent to CCL by: "Alfredo Tlahuice" [tlahuicef~!~yahoo.com] It is a pleasure to invite you to join us at the 15th International Symposium on Small Particles and Inorganic Clusters (ISSPIC-XV) to be held on September 19-24, 2010 in Oaxaca City, Mexico. http://www.fisica.unam.mx/garzon/isspic15/committees.html The abstract deadline to request oral presentation (hot topics) is 1st May, while the poster presentation is 15th May. We hope to see you on ISSPIC XV. Alfredo Tlahuice Organizing Committee From owner-chemistry@ccl.net Thu Apr 29 16:50:00 2010 From: "Jamin Krinsky jamink]![berkeley.edu" To: CCL Subject: CCL:G: MP2 failure Message-Id: <-41747-100429130145-8466-Jj3cCTCu2GR0k5nchXhLog[]server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=UTF-8 Date: Thu, 29 Apr 2010 10:01:34 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink * berkeley.edu] Dear Jane, Yes, in this case it's better to do the optimization, then do the frequency calculation after. This way you can troubleshoot the frequency calculation without redoing the optimization each time. Full MP2 frequencies are quite resource hungry, often a system that works fine for energies and gradients will be totally insufficient for computing forces (a frequency calculation). I don't know how big your molecule is or what kind of system you're running on, but a lack of hard disk space is most likely your issue. We've got 450GB of available scratch space on our cluster nodes and we're seeing people having problems running MP2 frequencies with 40 atoms / 600 basis functions. Some other programs have local MP2 implementations that might work better for you, maybe someone here can suggest a good (free) one to try out. Regards, Jamin 2010/4/28 =E6=AE=B7=E5=81=A5 janeyin600_._gmail.com : > Hi there, > > I have some trouble with calculating=C2=A0some MP2=C2=A0jobs recently. I= =C2=A0found > that=C2=A0the combination of "opt=C2=A0freq" will=C2=A0automatically gene= rate=C2=A0a link after > the energy has converged: > > =C2=A0Normal termination of Gaussian 03 at Wed Apr 28 06:22:56 2010. > =C2=A0Link1:=C2=A0 Proceeding to internal job step number=C2=A0 2. > =C2=A0-------------------------------------------------------------------= - > =C2=A0#N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk UMP2(FC)/6-31G(= d) Freq > and then it will continue to run for a while. For most=C2=A0MP2 jobs I am= now > carrying on, it finished the first step, but failed at the second step. I= am > now separating "freq" and "opt" commands. Don't know if that works... > > Any advice? Thank you very much~~ > > Jane --=20 Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink * berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Thu Apr 29 17:25:00 2010 From: "John W Daily john.daily-$-colorado.edu" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41748-100429113818-8522-wsqHhLf0JCwkeWHKwZ2CXQ-$-server.ccl.net> X-Original-From: John W Daily Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Thu, 29 Apr 2010 09:05:45 -0600 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: John W Daily [john.daily..colorado.edu] I'm pretty sure Chicken of the VNC works. On Apr 29, 2010, at 5:07 AM, Joe Leonard jleonard42/agmail.com wrote: >=20 > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] > Folks, >=20 > Has anybody successfully used remote desktop software from a Mac (Snow = Leopard) to a headless PC (Windows XP or 7), especially for running 3D = graphics such as PyMOL? While I am a mac-o-phile, there are various = programs that aren't available that I am interested in. There are also = a lot of interesting little machines appearing (Nvidia ION desktops, = etc). If I could have the machine and not have to worry about KVM = switching, that would be a win. >=20 > What software did you use, and did it work over WIFi or was a cable = connection required? Inquiring minds want to know! >=20 > Thanks in advance! >=20 > Joe Leonard > jleonard42[]gmail.com > -- > Is the question "Where do babies come from?" really a science = question? Yes. Geography to be specific. Croydon to be precise. >=20 >=20 >=20 > - This is automatically added to each message by the mailing script =3D-= > To recover the email address of the author of the message, please = change>=20>=20>=20>=20>=20> Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 From owner-chemistry@ccl.net Thu Apr 29 17:59:01 2010 From: "Soren Eustis soreneustis###gmail.com" To: CCL Subject: CCL:G: MP2 failure Message-Id: <-41749-100429131635-24157-gvYzmRPICXn7A6GVaHdnhA%%server.ccl.net> X-Original-From: Soren Eustis Content-Transfer-Encoding: 7bit Content-Type: multipart/alternative; boundary=Apple-Mail-50-48961459 Date: Thu, 29 Apr 2010 19:17:00 +0200 Mime-Version: 1.0 (iPhone Mail 7E18) Sent to CCL by: Soren Eustis [soreneustis]^[gmail.com] --Apple-Mail-50-48961459 Content-Type: text/plain; charset=utf-8; format=flowed; delsp=yes Content-Transfer-Encoding: quoted-printable This does not seem like an error. Gaussian is just creating a new job =20= with the optimized geometry. It may seem like it is not doing =20 anything, but drew jobs can take much longer than opt jobs in some =20 cases. Or, perhaps I am misinterpreting your problem. Does Gaussian give you =20= an error termination message? Regards, Soren Eustis ETH - Zurich On 29.04.2010, at 07:53, "=E6=AE=B7=E5=81=A5 janeyin600_._gmail.com" = wrote: > Hi there, > > I have some trouble with calculating some MP2 jobs recently. I found =20= > that the combination of "opt freq" will automatically generate a =20 > link after the energy has converged: > > Normal termination of Gaussian 03 at Wed Apr 28 06:22:56 2010. > Link1: Proceeding to internal job step number 2. > -------------------------------------------------------------------- > #N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk UMP2(FC)/6-31G(d) = Freq > and then it will continue to run for a while. For most MP2 jobs I am =20= > now carrying on, it finished the first step, but failed at the =20 > second step. I am now separating "freq" and "opt" commands. Don't =20 > know if that works... > > Any advice? Thank you very much~~ > > Jane --Apple-Mail-50-48961459 Content-Type: text/html; charset=utf-8 Content-Transfer-Encoding: quoted-printable
This does not seem like an error. =  Gaussian is just creating a new job with the optimized geometry. =  It may seem like it is not doing anything, but drew jobs can take = much longer than opt jobs in some cases.

Or, = perhaps I am misinterpreting your problem.  Does Gaussian give you = an error termination = message?

Regards,

Soren = Eustis
ETH - Zurich



On = 29.04.2010, at 07:53, "=E6=AE=B7=E5=81=A5 janeyin600_._gmail.com" <owner-chemistry : ccl.net> = wrote:

Hi = there,
 
I have some trouble = with calculating some MP2 jobs recently. I found = that the combination of "opt freq" will automatically = generate a link after the energy has converged:
 
 Normal termination of Gaussian 03 at Wed = Apr 28 06:22:56 2010.
 Link1:  Proceeding to internal job = step number  2.
=  --------------------------------------------------------------------=
 #N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk = UMP2(FC)/6-31G(d) Freq
and then it = will continue to run for a while. For most MP2 jobs I am now = carrying on, it finished the first step, but failed at the second step. = I am now separating "freq" and "opt" commands. Don't know if that = works...
 
Any advice? Thank you = very much~~
 
Jane
= --Apple-Mail-50-48961459-- From owner-chemistry@ccl.net Thu Apr 29 18:35:00 2010 From: "Alex Allardyce aa=-=chemaxon.com" To: CCL Subject: CCL: Bulding a Chemical database Message-Id: <-41750-100429130016-6929-KTWeCEcyTYKQHmSNpsfPnA,+,server.ccl.net> X-Original-From: Alex Allardyce Content-Type: multipart/alternative; boundary="------------010102060405080704030409" Date: Thu, 29 Apr 2010 18:12:48 +0200 MIME-Version: 1.0 Sent to CCL by: Alex Allardyce [aa-$-chemaxon.com] This is a multi-part message in MIME format. --------------010102060405080704030409 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit HI Ronald, I would suggest ChemAxon things of course, excuse the pitch. JChem Base toolkit will be good if you want to build up a platform which is flexible/extend-able etc. As far as database engines go, we find MYSQL is fine and some of our users, with very heavy demands (hundreds of millions of rows), have success with POSTGRE, we have a cartridge for Oracle if you want to go that way also. If you don't want to build your own and want something out of the box you can use Instant JChem, a desktop application, to do this - it is really very powerful and especially good with dynamically populating property predictions. This is a nice potential solution because you can deploy quickly, it does have an API (application programming interface) so you can tune somewhat and if you need more flexibility (also build web pages etc) you are quite free to use the toolkit along side it, infact the same database table even. If you are thinking of user acceptance/compliance you should also not exclude an Excel product, if the users know it then it can be Looking at the TDA website I cannot say that this is free (as I usually do when responding to academics here) since you are commercial but you can download and evaluate freely. Hope this is useful Alex Links * *JChem Base* for structure and reaction searching and database handling, including Markush search * *JChem Cartridge* for Oracle® database integration, * *Standardizer* for structure canonicalisation, * *Instant JChem * desktop application for local and remote structure database management, search and prediction * *JChem for Excel * enabling chemistry in Excel Also ** * * Calculator Plugins* for prediction of various properties based on structure, * *JChem Web Services* a web services integration interface Relevant user presentations* * 1. *Cost effective cheminformatics for small chemistry teams integrated within larger discovery groups *: John McNeil (John McNeil & Co) 2. *Building a RESTful DrugBank Structure Resource Using Ruby on Rails and JChem Base : *Craig Knox (University of Alberta) 3. *Developing with ChemAxon at Evotec - some case studies. *Catherine Reisser (Evotec) 4. *ChemAxon and an Electronic Research Habitat at the Biopolis Experimental Research Centre : *Peter Condron (A*STAR) 5. *Palatin Technologies' Cheminformatics Solution. *Jim Bullington (Palatin Technologies) On 4/28/2010 7:55 PM, Ronald L Cook cookrl%a%tda.com wrote: > Sent to CCL by: "Ronald L Cook" [cookrl() tda.com] > Hi All > > We are carrying out a comprehensive computational study of a series of molecules including optimization and property calculations at the RB3LYP 6-311++F(d,p) level to generate QM descriptors. We are also calculating MEP maps, charges on atoms, and Fukui indices using Hirshfeld population analysis. We would also like to store graphics of the the optimized structures. > > When we started out we were using Excel to store and probe the results. This has gotten quite unwieldly. Does anyone have any recommendations for the best database software (e.q. Access or software more directed to chemists)? Or can anyone recommend a good book on building a chemical database from Access or the various forms of SQL software. > > Thanks in Advance for your advise > > Ronald Cook > Principal Scientist > TDA research, Inc.> > > --------------010102060405080704030409 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit HI Ronald,

I would suggest ChemAxon things of course, excuse the pitch.

JChem Base toolkit will be good if you want to build up a platform which is flexible/extend-able etc. As far as database engines go, we find MYSQL is fine and some of our users, with very heavy demands (hundreds of millions of rows), have success with POSTGRE, we have a cartridge for Oracle if you want to go that way also.

If you don't want to build your own and want something out of the box you can use Instant JChem, a desktop application, to do this - it is really very powerful and especially good with dynamically populating property predictions. This is a nice potential solution because you can deploy quickly, it does have an API (application programming interface) so you can tune somewhat and if you need more flexibility (also build web pages etc) you are quite free to use the toolkit along side it, infact the same database table even.

If you are thinking of user acceptance/compliance you should also not exclude an Excel product, if the users know it then it can be

Looking at the TDA website I cannot say that this is free (as I usually do when responding to academics here) since you are commercial but you can download and evaluate freely.

Hope this is useful
Alex

Links
  • JChem Base for structure and reaction searching and database handling, including Markush search
  • JChem Cartridge for Oracle® database integration,
  • Standardizer for structure canonicalisation,
  • Instant JChem desktop application for local and remote structure database management, search and prediction
  • JChem for Excel enabling chemistry in Excel
Also
Relevant user presentations
  1. Cost effective cheminformatics for small chemistry teams integrated within larger discovery groups: John McNeil (John McNeil & Co)
  2. Building a RESTful DrugBank Structure Resource Using Ruby on Rails and JChem Base: Craig Knox (University of Alberta)
  3. Developing with ChemAxon at Evotec - some case studies. Catherine Reisser (Evotec)
  4. ChemAxon and an Electronic Research Habitat at the Biopolis Experimental Research Centre: Peter Condron (A*STAR)
  5. Palatin Technologies’ Cheminformatics Solution. Jim Bullington (Palatin Technologies)




On 4/28/2010 7:55 PM, Ronald L Cook cookrl%a%tda.com wrote: 
Sent to CCL by: "Ronald L Cook" [cookrl() tda.com]
Hi All

We are carrying out a comprehensive computational study of a series of molecules including optimization and property calculations at the RB3LYP 6-311++F(d,p) level to generate QM descriptors.  We are also calculating MEP maps, charges on atoms, and Fukui indices using Hirshfeld population analysis.  We would also like to store graphics of the the optimized structures.

When we started out we were using Excel to store and probe the results.  This has gotten quite unwieldly.  Does anyone have any recommendations for the best database software (e.q. Access or software more directed to chemists)?  Or can anyone recommend a good book on building a chemical database from Access or the various forms of SQL software.

Thanks in Advance for your advise

Ronald Cook
Principal Scientist
TDA research, Inc.E-mail to subscribers: CHEMISTRY . ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST . ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
--------------010102060405080704030409-- From owner-chemistry@ccl.net Thu Apr 29 19:10:00 2010 From: "V Gossen Verena.Gossen,+,web.de" To: CCL Subject: CCL:G: g09 charge of metal atoms in complexes Message-Id: <-41751-100429122216-19250-YaXZhadrSltCN3UFOQTtwg ~ server.ccl.net> X-Original-From: "V Gossen" Date: Thu, 29 Apr 2010 12:22:15 -0400 Sent to CCL by: "V Gossen" [Verena.Gossen###web.de] Hi there, I wonder if there is a possibility to locate charges on specific atoms with gaussian 09. I normally use the keyword MHFx for the metal. For example MHF10 for Ti. # Becke3LYP/Gen Pseudo=Read Opt Test Ti 0 3 Ti 0.0 0.0 0.0 molecule specification continues C O H 0 TZVP **** Ti 0 SDD **** Ti 0 MHF10 where do I have to specify the charge (+IV) for Ti? Any advice? Thank you very much Verena From owner-chemistry@ccl.net Thu Apr 29 19:45:01 2010 From: "Alfredo Tlahuice tlahuicef||fisica.unam.mx" To: CCL Subject: CCL: ISSPIC XV abstracts submissions Message-Id: <-41752-100429114922-18150-Ez4hQe9nGfmDy4sqyS8QRA**server.ccl.net> X-Original-From: "Alfredo Tlahuice" Date: Thu, 29 Apr 2010 11:49:05 -0400 Sent to CCL by: "Alfredo Tlahuice" [tlahuicef{=}fisica.unam.mx] It is a pleasure to invite you to join us at the 15th International Symposium on Small Particles and Inorganic Clusters (ISSPIC-XV) to be held on September 19-24, 2010 in Oaxaca City, Mexico. http://www.fisica.unam.mx/garzon/isspic15/committees.html The abstract deadline to request oral presentation (hot topics) is 1st May, while the poster presentation is 15th May. We hope to see you on ISSPIC XV. Alfredo Tlahuice Organizing Committee From owner-chemistry@ccl.net Thu Apr 29 20:20:01 2010 From: "Naudis Antonio De Voz ndev{:}unicartagena.edu.co" To: CCL Subject: CCL: how I can model for a protein homology? Message-Id: <-41753-100429124706-27187-pxs5hUKtYdTk6KoZ1H85lQ|-|server.ccl.net> X-Original-From: "Naudis Antonio De Voz" Date: Thu, 29 Apr 2010 12:47:04 -0400 Sent to CCL by: "Naudis Antonio De Voz" [ndev^unicartagena.edu.co] is that I've been reading about by homology modeling proteins , but I could not find a clear methodology ... and I really want to know how to build a theoretical model, since I need one for a study... thanks very much From owner-chemistry@ccl.net Thu Apr 29 20:54:00 2010 From: "Heath Watts hdw115*|*psu.edu" To: CCL Subject: CCL:G: MP2 failure Message-Id: <-41754-100429151544-31811-yDgS9mZjHVKqnOFjb4M0/Q---server.ccl.net> X-Original-From: Heath Watts Content-Type: multipart/alternative; boundary=000e0cd2924a66d2eb048564f34c Date: Thu, 29 Apr 2010 15:15:33 -0400 MIME-Version: 1.0 Sent to CCL by: Heath Watts [hdw115[*]psu.edu] --000e0cd2924a66d2eb048564f34c Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Jane, Try using more MaxDisk space, more processors, and more memory. If your frequency job stops (assuming you're using Gaussian 03), the job will have to restart from the beginning, because MP2 calculates frequencies analytically rather than numerically; therefore, if the job stops, it won't restart from the last freq calculation step.If you are using G09, you can restart a frequency calculation. Our group was recently working on a 51-ato= m model showing the intermolecular interaction between an amino acid and a monosaccharide. Using MP2/6-31(d), the job kept dying when we tried to run it with 16 processors, 8GB or memory, and MaxDisk=3D8GB. We were ultimately able to do the calculation in just three days using 32 processors, 128GB or memory, and MaxDisk=3D500GB. I think that the calculation was finally successful due to the amount of MaxDisk and memory that we were able to allocate to the job. MP2 makes some very large checkpoint and temporary files when it does frequency calculations, so it needs plenty of MaxDisk space. Good luck. Best, Heath 2010/4/29 =E6=AE=B7=E5=81=A5 janeyin600_._gmail.com > Hi there, > > I have some trouble with calculating some MP2 jobs recently. I found > that the combination of "opt freq" will automatically generate a link aft= er > the energy has converged: > > Normal termination of Gaussian 03 at Wed Apr 28 06:22:56 2010. > Link1: Proceeding to internal job step number 2. > -------------------------------------------------------------------- > #N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk UMP2(FC)/6-31G(d) Fr= eq > and then it will continue to run for a while. For most MP2 jobs I am now > carrying on, it finished the first step, but failed at the second step. I= am > now separating "freq" and "opt" commands. Don't know if that works... > > Any advice? Thank you very much~~ > > Jane > --000e0cd2924a66d2eb048564f34c Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Hi Jane,
Try using more MaxDisk space, more processors, and more memory.= If your frequency job stops (assuming you're using Gaussian 03), the j= ob will have to restart from the beginning, because MP2 calculates frequenc= ies analytically rather than numerically; therefore, if the job stops, it w= on't restart from the last freq calculation step.If you are using G09, = you can restart a frequency calculation. Our group was recently working on = a 51-atom model showing the intermolecular interaction between an amino aci= d and a monosaccharide. Using MP2/6-31(d), the job kept dying when we tried= to run it with 16 processors, 8GB or memory, and MaxDisk=3D8GB. We were ul= timately able to do the calculation in just three days using 32 processors,= 128GB or memory, and MaxDisk=3D500GB. I think that the calculation was fin= ally successful due to the amount of MaxDisk and memory that we were able t= o allocate to the job. MP2 makes some very large checkpoint and temporary f= iles when it does frequency calculations, so it needs plenty of MaxDisk spa= ce. Good luck.
Best,
Heath

2010/4/29 =E6=AE=B7=E5=81= =A5 janeyin600_._gmail.com <owner-chemistry|,|ccl.net>
Hi there,
=C2=A0
I have some trouble wi= th calculating=C2=A0some MP2=C2=A0jobs recently. I=C2=A0found that=C2=A0the= combination of "opt=C2=A0freq" will=C2=A0automatically generate= =C2=A0a link after the energy has converged:
=C2=A0
=C2=A0Normal termi= nation of Gaussian 03 at Wed Apr 28 06:22:56 2010.
=C2=A0Link1:=C2=A0 Pr= oceeding to internal job step number=C2=A0 2.
=C2=A0--------------------------------------------------------------------<= br>=C2=A0#N Geom=3DAllCheck Guess=3DRead SCRF=3DCheck GenChk UMP2(FC)/6-31G= (d) Freq
and then it will= continue to run for a while. For most=C2=A0MP2 jobs I am now carrying on, = it finished the first step, but failed at the second step. I am now separat= ing "freq" and "opt" commands. Don't know if that w= orks...
=C2=A0
Any advice? Thank you very= much~~
=C2=A0
Jane

--000e0cd2924a66d2eb048564f34c-- From owner-chemistry@ccl.net Thu Apr 29 21:30:02 2010 From: "xunlei ding dingxunlei * gmail.com" To: CCL Subject: CCL:G: [GaussView] Can GaussView 5 draw the ECD spectra directly? Message-Id: <-41755-100429191620-8335-NY27tO5Q59gzTll3edI9WA-x-server.ccl.net> X-Original-From: xunlei ding Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=GB2312 Date: Fri, 30 Apr 2010 07:16:13 +0800 MIME-Version: 1.0 Sent to CCL by: xunlei ding [dingxunlei(a)gmail.com] Dear All, I want to simulate an ECD spectra by G03 with TDDFT calculations. Can it be shown in GaussView 5 ? Or how can I draw it from the log file of G03? Thank you! --=20 ------------------------------------------------------ Xun-Lei Ding (=B6=A1=D1=B8=C0=D7) Associate Research Professor of Physical Chemistry, Ph.D State Key Lab for Struct. Chem. of Unstable and Stable Species Institute of Chemistry, Chinese Academy of Sciences Zhongguancun North First Street 2=A3=AC Beijing 100190, P. R. China Phone 86-10-62568330 Fax 86-10-62559373 From owner-chemistry@ccl.net Thu Apr 29 22:33:01 2010 From: "Igor Filippov Contr filippovi_._mail.nih.gov" To: CCL Subject: CCL: Mac/Windows remote desktop question Message-Id: <-41756-100429164048-15506-Y1mcJdjh87nID/ukXR2+og|server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="UTF-8" Date: Thu, 29 Apr 2010 16:03:50 -0400 MIME-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [filippovi*|*mail.nih.gov] Just saw it today - http://infoworld.com/d/mobilize/infoworld-review-free-remote-access-tools-windows-and-mac-018 Igor P.S. Not sure what kind of work would require gigabit ethernet. I'm connecting using Remote Desktop from home. Works fine over 2Mbps (or whatever Comcast is letting me use this days). I wouldn't recommend 3D graphics over the net though of course. On Thu, 2010-04-29 at 08:52 -0400, David Watson dewatson^olemiss.edu wrote: > Sent to CCL by: David Watson [dewatson,+,olemiss.edu] > On Apr 29, 2010, at 6:07 AM, Joe Leonard jleonard42/agmail.com wrote: > > > > > Sent to CCL by: Joe Leonard [jleonard42|gmail.com] > > Folks, > > > > Has anybody successfully used remote desktop software from a Mac (Snow Leopard) to a headless PC (Windows XP or 7), especially for running 3D graphics such as PyMOL? While I am a mac-o-phile, there are various programs that aren't available that I am interested in. There are also a lot of interesting little machines appearing (Nvidia ION desktops, etc). If I could have the machine and not have to worry about KVM switching, that would be a win. > > > > I don't understand why you would want to run PyMOL remotely as there is a perfectly fine implementation for Mac OS X already available from exactly the same source. > As to the matter of running programs remotely on a headless PC, I have found much success with the free "Remote Desktop Connection" software available from Microsoft. > RDC runs fairly smoothly, and you can customize the graphics for full-screen usage if you wish. > > Another alternative is to use LogMeIn from logmein.com, although you may need to navigate around for a while to locate the free version. > This option requires that you install software on both the "server" and the "client", so that may or may not be an acceptable solution to you. > > Both of these options are going to be a little clunky if you are trying to visualize and display complex macromolecules in "ball & stick" or "surface" modes, as there will be quite a lot of graphical information being updated if you wish to translate or rotate the molecule. > It's sort of the same story if you use XQuartz and X11 windowing to a remote Linux or Unix server. > > > > What software did you use, and did it work over WIFi or was a cable connection required? Inquiring minds want to know! > > > > You won't be able to do modeling without a high speed connection. > Gigabit ethernet is the way to go, unless by some magical chance you have a fiber network card in your mac and a fiber switch in your lab. > Of course you can remotely log-in over wireless, but I think you will soon tire of the time it takes to get any work accomplished. > > > > -=is is automatically added to each message by the mailing script => > From owner-chemistry@ccl.net Thu Apr 29 23:17:01 2010 From: "Jian Wang computationalboy . gmail.com" To: CCL Subject: CCL: Protein structure prediction through fold recognition Message-Id: <-41757-100429104341-20833-kC3jADUAzy4UQ8MwUVg/HA{}server.ccl.net> X-Original-From: Jian Wang Content-Type: multipart/alternative; boundary=000e0cd71a5ac54d2104856060b2 Date: Thu, 29 Apr 2010 21:48:13 +0800 MIME-Version: 1.0 Sent to CCL by: Jian Wang [computationalboy!=!gmail.com] --000e0cd71a5ac54d2104856060b2 Content-Type: text/plain; charset=ISO-8859-1 Dear all: Can anyone recommend some program for protein fold recognition from a primary sequence? I can not find good homology protein for my target sequence. Thanks in advance! -- Jian Wang (Arthur) Shenyang Pharmaceutical University P.O. Box 40 103 Wenhua Road, Shenhe District Shenyang,110016, P. R. China Tel : +86 24 23986419 Fax: +86 24 23995043 E-Mail: computationalboy(at)gmail.com --000e0cd71a5ac54d2104856060b2 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable

Dear all:
Can anyone recommend some prog= ram for protein fold recognition from a primary sequence?
I can n= ot find good homology protein for my target sequence.
Thanks in a= dvance!

--000e0cd71a5ac54d2104856060b2--