From owner-chemistry@ccl.net Wed May 14 00:05:00 2008 From: "Babarao Ravichandar ravichandar[A]nus.edu.sg" To: CCL Subject: CCL: DL_POLY electric field Message-Id: <-36956-080513231314-30601-2hOr27a7oHdOIwV9IU7jjQ#%#server.ccl.net> X-Original-From: "Babarao Ravichandar" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="us-ascii" Date: Wed, 14 May 2008 10:40:31 +0800 MIME-Version: 1.0 Sent to CCL by: "Babarao Ravichandar" [ravichandar * nus.edu.sg] Hi, Can anyone tell me how to include the flexibility in the framework using DL_POLY. How to modify the field file to include the bonded parameters. Kindly help me in this regards Ravichandar=20 -----Original Message----- > From: owner-chemistry-#-ccl.net [mailto:owner-chemistry-#-ccl.net]=20 Sent: Wednesday, May 14, 2008 8:23 AM To: Babarao Ravichandar Subject: CCL: DL_POLY electric field Sent to CCL by: John W Daily [john.daily++colorado.edu] Nicola, You must have three lines. The following imposes an electric field of 5.0 (kcal units) in the x-dir. extern elec 5.0 0.0 0.0 And be sure to get the units right. They depend on the units you are using in the FIELD file. John On May 13, 2008, at 10:03 AM, Nicola Salvi nicolasalvi _ email.it wrote: > > Sent to CCL by: "Nicola Salvi" [nicolasalvi{=3D}email.it] I have a=20 > problem with DL_POLY. I have to understand how to set up an external=20 > electric field in my simulation, parallel to z-axis. I know that I=20 > have to use elec command in FIELD file, but that's all I was able to=20 > find out, it still continues to output me error 52 and I didn't find=20 > much on web! > Thanks all for your help! > > > > -=3D 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> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: =20 > search)> > -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20http://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Wed May 14 04:04:01 2008 From: "Nick Isachenkov i.nick[*]mail.ru" To: CCL Subject: CCL:G: GAUSSIAN: "locking" the desired MO configuration when the 'guess= Message-Id: <-36957-080514040037-14072-IvAJbr+Q0jbpCp5LDjYSvA+/-server.ccl.net> X-Original-From: "Nick Isachenkov" Date: Wed, 14 May 2008 04:00:31 -0400 Sent to CCL by: "Nick Isachenkov" [i.nick],[mail.ru] See help guide to Gaussian: Guess->alter: Indicates that the orbitals selected for occupation in the Hartree-Fock wavefunction should not be those of lowest energy. Normally, the occupied orbitals are selected as those with lowest eigenvalues for the one-electron Hamiltonian used in the initial guess programs. The alteration sections consist of a set of transpositions indicating that one of these occupied orbitals is to be replaced by one of the other (virtual) orbitals. Each such transposition is on a separate line and has two integers N1 and N2 (free format, separated by spaces or a comma as usual) indicating that orbital N1 is to be swapped with orbital N2. The list of orbital transpositions is terminated by the blank line at the end of the input section. For UHF calculations, two such orbital alteration sections are required, the first specifying transpositions of orbitals, and the second specifying transpositions of orbitals. Both sections are always required. [b]Thus, even if only transpositions are needed, the section is required even though it is empty (and vice-versa). The second blank line to indicate an empty section must be included. [/b] From owner-chemistry@ccl.net Wed May 14 08:18:00 2008 From: "Raj S r.subramanian!A!ipc.uni-stuttgart.de" To: CCL Subject: CCL: optimization problems Message-Id: <-36958-080514081624-30625-F8MrUIawu1/bKScXRlizng=server.ccl.net> X-Original-From: "Raj S" Date: Wed, 14 May 2008 08:16:20 -0400 Sent to CCL by: "Raj S" [r.subramanian===ipc.uni-stuttgart.de] Hi, I am trying to optimize geometry of a transition metal complex. The job got aborted by several repeated 'Restarting incremental fock formation' But some where in the middle/last step of optimization i got one 'YES' (RMS Force is converged)..after this YES...my job aborted by ending with several 'Restarting incremental fock formation'... In the Book, Exploring chemistry with ... its mentioned that including CalcFc from the step where i got one 'YES' is recommended. But there are two orientations....I dont know which one to select...Input of standard orientation??? Thanks for your reply, raja From owner-chemistry@ccl.net Wed May 14 08:52:00 2008 From: "igma sanjaya igmass-#-gmail.com" To: CCL Subject: CCL: need 3 - month training in computation chemistry and molecular modeling Message-Id: <-36959-080514013622-26658-Oh2gqyuP9qm8a9FntnZt+w]~[server.ccl.net> X-Original-From: "igma sanjaya" Content-Type: multipart/alternative; boundary="----=_Part_10193_9314571.1210739803389" Date: Wed, 14 May 2008 11:36:43 +0700 MIME-Version: 1.0 Sent to CCL by: "igma sanjaya" [igmass(~)gmail.com] ------=_Part_10193_9314571.1210739803389 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear Sir/Madam I will initiate learning computation chemistry and chemical modeling. So many software, free or lycense, out there that make me difficult as beginner. I wish there are 3-6 month training for starting activities to take-over skill in operating those software. So in the next time the skill usefull for supporting my research in chemistry like in transport processing, molecular dynamic, enzyme and macromolecule modelling, etc. Would any body give me information about the training complete with the place, time, anual fee, accomodation, and so on for the last of this year or beginning of the next years. Thankyou for your information. ------=_Part_10193_9314571.1210739803389 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Dear Sir/Madam
 
I will initiate learning computation chemistry and chemical modeling. So many software, free or lycense, out there that make me difficult as beginner. I wish there are 3-6 month training for starting activities to take-over skill in operating those software. So in the next time the skill usefull for supporting my research in chemistry like in transport processing, molecular dynamic, enzyme and macromolecule modelling, etc.
Would any body give me information about the training complete with the place, time, anual fee, accomodation, and so on for the last of this year or beginning of the next years.
 
Thankyou for your information.
------=_Part_10193_9314571.1210739803389-- From owner-chemistry@ccl.net Wed May 14 12:10:00 2008 From: "David Hughes dwhfelice-x-gmail.com" To: CCL Subject: CCL: New software for searching the web for chemical information Message-Id: <-36960-080514120035-6788-dttFXCZCQ7JFRv3q5So+OA]-[server.ccl.net> X-Original-From: "David Hughes" Content-Type: multipart/alternative; boundary="----=_Part_1349_19451572.1210777535035" Date: Wed, 14 May 2008 17:05:34 +0200 MIME-Version: 1.0 Sent to CCL by: "David Hughes" [dwhfelice]![gmail.com] ------=_Part_1349_19451572.1210777535035 Content-Type: text/plain; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi, Tony. For some reason I didn't originally get your message, asking me about my posting, so apologies for the delay. You asked about the advantages that I saw, from my point of view, of CWM GlobalSearch. There are four that come quickly to mind: > The ability to search over multiple sources with a single search. As you rightly point out, there is a lot of overlap between some of the sources being searched, but that may simply be unavoidable these days. In any case, the fact that I can launch a single search, and get back a set of organized results, appeals to me. > The ability to submit several queries at once, using SDfiles. I really like being able to pull together a set of specific query structures (like a= s not related to one another) and, again, submitting a single search. The results come back organized by the individual query structures. > The ability to "fine tune" the sources that will be searched. Not all sources "out there" are equal. It's possible with GlobalSearch to make the decision that, for certain searches, specific sources should (or should not= ) be considered. You can save the profiles for those searches, so that you ca= n reuse them later, once you're happy with a given profile (or profiles) -- that's a plus. > The ability to quickly determine the sources of search results. The summary table of results that comes back from a search includes information about how many results came from a given source, which is useful when deciding where to start "drilling down" for actual data. The question about the real number of unique structures one can reach this way is tough to answer, I know. I really don't know what the number of unique structures "out there" would be, though your estimate sounds pretty good. In any case, I'm not taking the absolute number as quite so important as the general sense of being able to search over "all" the free sources. (There is a fee for using CWM GlobalSearch beyond the trial period, but at EUR 120 / year, this is pretty close to "free".) Of course, there are a lot of excellent "for fee" sources out there that on= e needs to consider when trying to do a comprehensive search. But for certain types of searches ("where can I get this?" "has this already been reported?= " "who else is working on this?" "how has this been commonly used?"), this is an excellent place to start. Cheers, David > From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net] Sent: Friday, May 09, 2008 1:35 AM Subject: CCL: New software for searching the web for chemical information David, I took an early look at this application and was asked whether we were okay with having ChemSpider as part of the search and I of course agreed in keeping with our recent Creative Commons announcement.here http://www.chemspider.com/blog/chemspider-adopts-creative-commons-licenses.= html . As a user of the system I am interested in your experiences relative to the online services such as ChemSpider, PubChem or the Chemical Structure Lookup Service. What are the advantages > from your point of view (please feel free to connect with me offline). One comment, and I am sure that people are aware of it, is that the advertised 100 million structures are of course not unique structures. The PubChem dataset is on ChemSpider and ChemSpider is on PubChem ( http://www.chemspider.com/blog/pubchem-deposition-of-chemspider-data-is-wel= l-underway-my-favorite-color-is-green.html). There is a lvery large amount of overlap between all of the datasets and I based on experience I would estimate the number of unique structures at around 25-30 million. Do you happen to know what the real number of unique structures is? Best wishes PS. There was an interesting article about ChemSpider published in Nature yesterday =96 these systems of "global chemistry searching" are growing in number. http://www.chemspider.com/blog/nature-writes-about-chemspider.html Antony Williams, URL: www.chemspider.com Email: antony.williams-*-chemspider.com Phone: (919) 341-8375 Mobile: (919) 201-1516 Fax: (919) 300-5321 CONFIDENTIALITY NOTICE Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If you are not an addressee, please inform the sender immediately or contac= t feedback-*-chemspider.com. > From: owner-chemistry-*-ccl.net [mailto:owner-chemistry-*-ccl.net] Sent: Thursday, May 08, 2008 9:33 AM To: Antony Williams Subject: CCL: New software for searching the web for chemical information A friend recently showed me an interesting chemistry application that I thought members of CCL would like to know about. This application searches over "all" chemical information that is freely-available on the web, including the internet itself, using a single search. It is quite easy to use -- you simply draw a chemical structure, and start a search. You can also use SDfiles to submit a series of compounds as separate queries, simplifying searches for starting materials or test compounds. The application is called "CWM Global Search". You can find information about it at http://www.akosgmbh.de/globalsearch/index.htm, including a movi= e showing the use of Global Search. I note that you can now use this application for free for 7 days -- a convenient way to see if it would be helpful to you. Cheers, David David Hughes Basel, Switzerland (Apologies for "cross-posting", but I really think this is useful software to consider.) ------=_Part_1349_19451572.1210777535035 Content-Type: text/html; charset=WINDOWS-1252 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline
Hi, Tony.
 
For some reason I didn't originally get you= r message, asking me about my posting, so apologies for the delay.
 
You asked about the advantages that I saw, from my point of = view, of CWM GlobalSearch. There are four that come quickly to mind:
>= ; The ability to search over multiple sources with a single search. As you = rightly point out, there is a lot of overlap between some of the sources be= ing searched, but that may simply be unavoidable these days. In any case, t= he fact that I can launch a single search, and get back a set of organized = results, appeals to me.
 
> The ability to submit several queries at once, using SDfiles= . I really like being able to pull together a set of specific query structu= res (like as not related to one another) and, again, submitting a single se= arch. The results come back organized by the individual query structures.  
> The ability to "fine tune" the sources that will b= e searched. Not all sources "out there" are equal. It's possi= ble with GlobalSearch to make the decision that, for certain searches, spec= ific sources should (or should not) be considered. You can save the profile= s for those searches, so that you can reuse them later, once you're hap= py with a given profile (or profiles) -- that's a plus.
 
> The ability to quickly determine the sources of search results. T= he summary table of results that comes back from a search includes inf= ormation about how many results came from a given source, which is useful w= hen deciding where to start "drilling down" for actual data.
 
The question about the real number of unique structures one can r= each this way is tough to answer, I know. I really don't know what the = number of unique structures "out there" would be, though your est= imate sounds pretty good. In any case, I'm not taking the absolute= number as quite so important as the general sense of being able to search = over "all" the free sources. (There is a fee for using CWM Global= Search beyond the trial period, but at EUR 120 / year, this is pretty close= to "free".)
 
Of course, there are a lot of excellent "for fee" sourc= es out there that one needs to consider when trying to do a comprehensive s= earch. But for certain types of searches ("where can I get this?"= "has this already been reported?" "who else is working on t= his?" "how has this been commonly used?"), this is an excell= ent place to start.
 
Cheers,
David
 
 
From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net]
Sent: Friday, May 09, 2008 1:3= 5 AM
Subject: CCL: New software for searching the web for chemical infor= mation
 
David,
I took an early look at this application and was asked = whether we were okay with having ChemSpider as part of the search and I of = course agreed in keeping with our recent Creative Commons announcement.here= http://www.chemspider.com/blog/chemspider-adopts-creative= -commons-licenses.html.
 
As a user of the system I am interested in your experiences relat= ive to the online services such as ChemSpider, PubChem or  the Chemica= l Structure Lookup Service. What are the advantages > from your point of= view (please feel free to connect with me offline).
 
One comment, and I am sure that people are aware of it, is that t= he advertised 100 million structures are of course not unique structures. T= he PubChem dataset is on ChemSpider and ChemSpider is on PubChem (http://www.chemspider.com/b= log/pubchem-deposition-of-chemspider-data-is-well-underway-my-favorite-colo= r-is-green.html). There is a lvery large amount of overlap between all = of the datasets and I based on experience I would estimate the number of un= ique structures at around 25-30 million. Do you happen to know what the rea= l number of unique structures is?
 
Best wishes
 
PS. There was an interesting article abo= ut ChemSpider published in Nature yesterday =96 these systems of "glob= al chemistry searching" are growing in number. http://www.chemspid= er.com/blog/nature-writes-about-chemspider.html
 
 
Antony Williams,
URL: www.chemspider.com
Email: antony.williams-*-chemspider.com
Phone: (919) 341-8375
Mobile: (= 919) 201-1516
Fax: (919) 300-5321
 
CONFIDENTIALITY NOTICE
Unless expressly= stated otherwise, this message is confidential and is intended for the add= ressee(s) only.
If you are not an addressee, please inform the sender im= mediately or contact feedback-*-chemspide= r.com.
 
 
From: owner-chemistry-*-ccl.= net [mailto:owner-chemistry-*-<= a href=3D"http://ccl.net">ccl.net]
Sent: Thursday, May 08, 2008 9:3= 3 AM
To: Antony Williams
Subject: CCL: New software for searching the web for chemical information 
A friend recently showed me an interesting chemistry applicatio= n that I thought members of CCL would like to know about. This application = searches over "all" chemical information that is freely-available= on the web, including the internet itself, using a single search. It is qu= ite easy to use -- you simply draw a chemical structure, and start a search= . You can also use SDfiles to submit a series of compounds as separate quer= ies, simplifying searches for starting materials or test compounds.
 
The application is called "CWM Global Search". You can = find information about it at http://www.akosgmbh.de/globalsearch/index.htm, including a = movie showing the use of Global Search. I note that you can now use this ap= plication for free for 7 days -- a convenient way to see if it would be hel= pful to you.
 
Cheers,
David
 
David Hughes
Basel, Switzerland<= br> 
(Apologies for "cross-posting", but I really think t= his is useful software to consider.)
------=_Part_1349_19451572.1210777535035-- From owner-chemistry@ccl.net Wed May 14 12:44:00 2008 From: "Jean-Christophe Poully poully**galilee.univ-paris13.fr" To: CCL Subject: CCL:G: Frequency calculation with ONIOM using UFF in the low level Message-Id: <-36961-080514101224-26292-YKGAkw9/wenP5ujG8ZJIEA:+:server.ccl.net> X-Original-From: Jean-Christophe Poully Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Wed, 14 May 2008 15:18:11 +0200 Mime-Version: 1.0 Sent to CCL by: Jean-Christophe Poully [poully .. galilee.univ-paris13.fr] Dear Bulumoni, If I were you, I would try replacing UFF by AM1,=20 it's much better for frequency calculations... If=20 your computer cannot do it, try UFF with charge=20 embedding, your structure should come closer to a=20 local minimum and the negative frequencies disappear... Hope it helps! JCP At 13:40 12/05/2008, you wrote: >Sent to CCL by: "Bulumoni Kalita" [bulumoni[]tezu.ernet.in] >Dear all, > I am facing a problem with the=20 > frequency calculation with the ONIOM option in=20 > Gaussian 03. I am using molecular mechanics=20 > UFF for the low level of calculation and=20 > B3LYP/6-31G(d,p) in the high level to check the=20 > C-O stretching frequeny of a adsorbed CO=20 > molecule in zeolite. I am getting number of=20 > negative frequencies upto as high as 1000 cm-1,=20 > although C-O stretching frequency is coming in=20 > the expected range. Is this result=20 > considerable? Or is there any method to get rid=20 > of these negative frequencies? Again I have=20 > checked a smaller zeolite cluster with=20 > B3LYP/6-31+G(d,p):RHF/3-21G, where all the=20 > frequencies are found to be positive. But we=20 > have limited computational facility to=20 > calculate the large zeolite cluster with=20 > B3LYP:RHF level. Can anyone please help me in solving the problem. > >Thanks in advance. > >Bulumoni Kalita >Research Scholar >Department of Chemical Sciences >Tezpur University >Assam, India Jean-Christophe Poully Doctorant dans l'=E9quipe AMIBES Laboratoire de Physique des Lasers Institut Galil=E9e 99, avenue JB Cl=E9ment 93430 VILLETANEUSE Bureau B002 0149403853=20 From owner-chemistry@ccl.net Wed May 14 13:26:00 2008 From: "M Qaiser Fatmi qaiser_fatmi*o*yahoo.com" To: CCL Subject: CCL:G: Angle force constant Message-Id: <-36962-080514125152-30914-fmzZuN+0ToVi1dYFAsVp/A%a%server.ccl.net> X-Original-From: "M Qaiser Fatmi" Date: Wed, 14 May 2008 12:51:48 -0400 Sent to CCL by: "M Qaiser Fatmi" [qaiser_fatmi-x-yahoo.com] Hi, I performed a geometry optimisation followed by a frequency calculations of Fe(II), complexed with three imidazole and one acetate group using gaussian 03. My question is regarding the calculation of angle force constant. Can anyone suggest me how to read the angle force constant from the gaussian output file. Thanking in advance Qaiser From owner-chemistry@ccl.net Wed May 14 13:54:00 2008 From: "Elaine Meng meng---cgl.ucsf.edu" To: CCL Subject: CCL: Active site visualization software Message-Id: <-36963-080514122205-13525-uP7lEtBqZDXMJ09U9u6PPA~!~server.ccl.net> X-Original-From: "Elaine Meng" Date: Wed, 14 May 2008 12:22:01 -0400 Sent to CCL by: "Elaine Meng" [meng- -cgl.ucsf.edu] > On May 13, 2008, at 12:48 AM, sobia ahsan halim sobia_halim],[yahoo.com wrote: > Can any one kindly let me know about the free protein's active site characterization, building and visualizer software. Thanks. Hi Sobia, UCSF Chimera has several features that relate, and it can be downloaded free for noncommercial use. Related features include finding contacts, finding hydrogen bonds, visualizing surface properties. If your structure is in the CASTp database, it will also fetch pocket volume/area information and display it in a table that interacts with the structure. There is not so much building, but you can replace sidechains with rotamers from the Dunbrack backbone-dependent or Richardson rotamer libraries. We are continually adding new features, so if you do download Chimera I recommend getting the May 1 snapshot http://www.cgl.ucsf.edu/chimera/download.html#snapshots or an even newer daily build: http://www.cgl.ucsf.edu/chimera/alpha-downloads.html The features are fully documented, and I just wrote a tutorial on binding site analysis that covers several of them and links to their respective manual pages: http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/index.html http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/squalene.html I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. meng]![cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html From owner-chemistry@ccl.net Wed May 14 14:29:00 2008 From: "Mike Towler mike_towler---vallico.net" To: CCL Subject: CCL: Tuscany QMC summer school Message-Id: <-36964-080514130244-8080-4SIkQgTnrMuCjQ9ThXSLHg*_*server.ccl.net> X-Original-From: "Mike Towler" Date: Wed, 14 May 2008 13:02:40 -0400 Sent to CCL by: "Mike Towler" [mike_towler~!~vallico.net] ----------------------------------------------------------------------- Summer workshops and schools at TTI, Vallico Sotto, Tuscany ----------------------------------------------------------------------- * "Quantum Monte Carlo in the Apuan Alps IV" - international conference Sat 26th July - Sat 2nd August 2008 (FULL) * "Quantum Monte Carlo and the CASINO program III" - summer school Sun 3rd - Sun 10th August 2008 (OPEN) * "Nucleic Acids function" - international workshop Sun 7th - Thu 11th September 2008 (FULL) * "KKR and many body applications" - international workshop Sat 13th - Thu 18th September 2008 (FULL) As there are still a few places available, the deadline for the QMC summer school has been extended from April 30th to June 15th. The original announcement for this event is below. Please contact the organizers (mdt26 at cam.ac.uk) if you would like to attend. Further details for all of these events, including registration information and lists of participants, can be found at : http://www.vallico.net/tti/tti.html --> PUBLIC EVENTS ------------------------------------------------------------------------- SUMMER SCHOOL ANNOUNCEMENT "Quantum Monte Carlo and the CASINO program III" ================================================ Sun 3rd August - Sun 10th August 2008 The Towler Institute, via del Collegio, Vallico Sotto, Tuscany, Italy http://www.vallico.net/tti/tti.html A4 POSTER FOR THE SCHOOL AVAILABLE HERE : http://www.vallico.net/tti/qmcatcp_08/poster.jpg The third international summer school in the series "Quantum Monte Carlo and the CASINO program" will take place during August 2008 in the TTI monastery in the Tuscan Apuan Alps, organized and hosted by members of Cambridge University physics department's Theory of Condensed Matter (TCM) Group. The aim of the school is to give students a thorough introduction to quantum Monte Carlo as a method for performing high-quality calculations of the electronic structure of real materials. The course is designed for young scientists who have no previous experience with this technique, though anyone interested is welcome to take part. Describing the complex behaviour of materials at the atomic level requires a sophisticated description of the correlated motion of the electrons. Quantum Monte Carlo (QMC) is an increasingly popular and explicitly many-body method with the unusual capability of yielding highly accurate results whilst also exhibiting a very favourable scaling of computational cost with system size. Over the last seventeen years, the Cambridge group have been researching QMC methods and we have created a powerful, general computer program - CASINO - to carry out the calculations. The school will focus both on the basic theory of QMC and on more advanced practical techniques, and will include a thorough introduction to the CASINO program. A background in density functional theory or similar is normally thought to be useful. The monastery is a delightful 16th century building incorporating an ancient church, and is situated in the isolated but spectacular setting of the Tuscan mountain village of Vallico Sotto. It is fully equipped with state of the art presentation and computer technology. All accommodation is on-site. A general policy imposed for all events at the Institute ensures that considerable time is set aside for mountain hikes, caving, canyon walking, swimming, eating in wonderful but cheap local restaurants, visiting nearby places of historical or artistic interest, and similar activities. Instructors will include a selection of the main authors of the CASINO program, (Prof. Richard Needs, Dr. Mike Towler, Dr. Neil Drummond, and Dr. Pablo Lopez Rios) and possibly others. Interested students should contact Mike Towler (mdt26 at cam.ac.uk) for registration and further details. ----------------------------------------------------------------------- "I will advice your school to anyone on the earth" (A FORMER STUDENT) ----------------------------------------------------------------------- From owner-chemistry@ccl.net Wed May 14 15:04:01 2008 From: "Daniel Robert Jones d.r.jones.1|*|warwick.ac.uk" To: CCL Subject: CCL:G: Using ECPs in place of PCs to build an electric field in gaussian 03 Message-Id: <-36965-080514112905-3054-LBCdP8qvmK2LLjwd8rfWwA**server.ccl.net> X-Original-From: "Daniel Robert Jones" Date: Wed, 14 May 2008 11:29:01 -0400 Sent to CCL by: "Daniel Robert Jones" [d.r.jones.1^warwick.ac.uk] Hi I am doing some work attempting to parameterise a tight-binding model for TiO2. I want to converge an SCF of a cluster of TiO2 embedded in an extended cluster of point charges, so the atoms in the centre of the cluster are representative of the bulk. Using +ve charges in place of Ti atoms is reported to cause unphysical polarisation of the O atoms at the edge of the cluster, and as such it has been suggested (e.g. Bredow, int. j. quant. chem., 1999(77), p127) that it is preferable to use an ECP instead of the point charges nearest the O atoms on the edge of the cluster. Is it possible to do this using gaussian 03? I have looked through the manual and searched on google for a bit and haven't found anything. But it doesn't seem like an unreasonable thing to want to do. What follows is the input file I am using to do a cluster embedded in point charges. If anyone could suggest how to change it to include these ECPs it would be most appreciated. Thanks Dan Jones ------- Gaussian 03 .com file input --------------------------- %chk=/home/msrbax/TiO2/bigcell/b3lyp/pc/hf/check/cluster.chk %mem=256mb #p hf gen pseudo=read gfinput IOP(3/33=1) pop=full punch=mo charge Cluster med. 0 , 1 O 5.9961958 1.4024658 0.0000000 Ti 4.5937300 4.5937300 0.0000000 O 5.4881292 3.6993308 -1.4790600 O 3.6993308 5.4881292 -1.4790600 O 5.4881292 3.6993308 1.4790600 O 3.6993308 5.4881292 1.4790600 O 5.9961958 1.4024658 -2.9581200 O 5.9961958 1.4024658 2.9581200 Ti 4.5937300 4.5937300 -2.9581200 Ti 4.5937300 4.5937300 2.9581200 Ti 6.8905950 2.2968650 -1.4790600 Ti 6.8905950 2.2968650 1.4790600 O 5.4881292 3.6993308 -4.4371800 O 3.6993308 5.4881292 -4.4371800 O 7.7849942 3.1912642 0.0000000 O 8.2930608 0.8943992 -1.4790600 O 8.2930608 0.8943992 1.4790600 O 5.9961958 5.9961958 0.0000000 Ti 6.8905950 2.2968650 -4.4371800 O 7.7849942 3.1912642 -2.9581200 O 7.7849942 3.1912642 2.9581200 O 5.9961958 5.9961958 -2.9581200 O 5.9961958 5.9961958 2.9581200 Ti 9.1874600 0.0000000 0.0000000 O 8.2930608 0.8943992 -4.4371800 Ti 9.1874600 0.0000000 -2.9581200 Ti 9.1874600 0.0000000 2.9581200 Ti 6.8905950 6.8905950 -1.4790600 Ti 6.8905950 6.8905950 1.4790600 O 8.2930608 5.4881292 -1.4790600 O 8.2930608 5.4881292 1.4790600 O 10.0818592 -0.8943992 -1.4790600 O 10.0818592 -0.8943992 1.4790600 Ti 9.1874600 4.5937300 0.0000000 O 10.5899258 1.4024658 0.0000000 Ti 9.1874600 4.5937300 -2.9581200 Ti 9.1874600 4.5937300 2.9581200 Ti 6.8905950 6.8905950 -4.4371800 O 10.0818592 3.6993308 -1.4790600 O 10.0818592 3.6993308 1.4790600 O 8.2930608 5.4881292 -4.4371800 O 7.7849942 7.7849942 0.0000000 O 10.0818592 -0.8943992 -4.4371800 O 10.5899258 1.4024658 -2.9581200 O 10.5899258 1.4024658 2.9581200 O 7.7849942 7.7849942 -2.9581200 O 7.7849942 7.7849942 2.9581200 O 10.0818592 3.6993308 -4.4371800 Ti 11.4843250 2.2968650 -1.4790600 Ti 11.4843250 2.2968650 1.4790600 O 10.5899258 5.9961958 0.0000000 O 10.5899258 5.9961958 -2.9581200 O 10.5899258 5.9961958 2.9581200 Ti 11.4843250 2.2968650 -4.4371800 O 12.3787242 3.1912642 0.0000000 Ti 9.1874600 9.1874600 0.0000000 O 12.3787242 3.1912642 -2.9581200 O 12.3787242 3.1912642 2.9581200 O 10.0818592 8.2930608 -1.4790600 O 8.2930608 10.0818592 -1.4790600 O 10.0818592 8.2930608 1.4790600 O 8.2930608 10.0818592 1.4790600 Ti 9.1874600 9.1874600 -2.9581200 Ti 9.1874600 9.1874600 2.9581200 Ti 11.4843250 6.8905950 -1.4790600 Ti 11.4843250 6.8905950 1.4790600 O 10.0818592 8.2930608 -4.4371800 O 8.2930608 10.0818592 -4.4371800 O 12.8867908 5.4881292 -1.4790600 O 12.8867908 5.4881292 1.4790600 Ti 11.4843250 6.8905950 -4.4371800 Ti 13.7811900 4.5937300 0.0000000 O 12.3787242 7.7849942 0.0000000 O 12.8867908 5.4881292 -4.4371800 Ti 13.7811900 4.5937300 -2.9581200 Ti 13.7811900 4.5937300 2.9581200 O 12.3787242 7.7849942 -2.9581200 O 12.3787242 7.7849942 2.9581200 O 14.6755892 3.6993308 -1.4790600 O 14.6755892 3.6993308 1.4790600 O 14.6755892 3.6993308 -4.4371800 O 0 6-31G **** Ti 0 lanl2dz **** Ti 0 lanl2dz 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9.18746000000000 0.00000000000000 -1.000000 4.59373000000000 9.18746000000000 0.00000000000000 -1.000000 -9.18746000000000 -4.59373000000000 0.00000000000000 -1.000000 -2.80493160000000 -10.9762584000000 2.95812000000000 -1.000000 -9.18746000000000 4.59373000000000 0.00000000000000 -1.000000 6.38252840000000 -10.9762584000000 2.95812000000000 -1.000000 10.9762584000000 2.80493160000000 2.95812000000000 -1.000000 10.9762584000000 -6.38252840000000 2.95812000000000 -1.000000 -5.99619580000000 1.40246580000000 8.87436000000000 2.000000 3.19126420000000 -7.78499420000000 -5.91624000000000 2.000000 -1.40246580000000 5.99619580000000 8.87436000000000 2.000000 7.78499420000000 -3.19126420000000 -5.91624000000000 2.000000 --------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed May 14 15:40:01 2008 From: "Igor Filippov Contr igorf~!~helix.nih.gov" To: CCL Subject: CCL: New software for searching the web for chemical information Message-Id: <-36966-080514144125-21020-JbmysGzLgSMkXNqIi9yUSQ-$-server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=Windows-1251 Date: Wed, 14 May 2008 14:01:54 -0400 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf * helix.nih.gov] I would like to point out that Chemical Structure Lookup Service has all of the before-mentioned capabilities and is absolutely free for everybody. The current count of the unique structures is 36 million structures from over a 100 different databases. You can access it here: http://cactus.nci.nih.gov/cgi-bin/lookup/new/search Thank you, Igor On Wed, 2008-05-14 at 17:05 +0200, David Hughes dwhfelice-x-gmail.com wrote: > Hi, Tony. > > For some reason I didn't originally get your message, asking me about > my posting, so apologies for the delay. > > You asked about the advantages that I saw, from my point of view, of > CWM GlobalSearch. There are four that come quickly to mind: > > The ability to search over multiple sources with a single search. As > you rightly point out, there is a lot of overlap between some of the > sources being searched, but that may simply be unavoidable these days. > In any case, the fact that I can launch a single search, and get back > a set of organized results, appeals to me. > > > The ability to submit several queries at once, using SDfiles. I > really like being able to pull together a set of specific query > structures (like as not related to one another) and, again, submitting > a single search. The results come back organized by the individual > query structures. > > > The ability to "fine tune" the sources that will be searched. Not > all sources "out there" are equal. It's possible with GlobalSearch to > make the decision that, for certain searches, specific sources should > (or should not) be considered. You can save the profiles for those > searches, so that you can reuse them later, once you're happy with a > given profile (or profiles) -- that's a plus. > > > The ability to quickly determine the sources of search results. The > summary table of results that comes back from a search includes > information about how many results came from a given source, which is > useful when deciding where to start "drilling down" for actual data. > > The question about the real number of unique structures one can reach > this way is tough to answer, I know. I really don't know what the > number of unique structures "out there" would be, though your estimate > sounds pretty good. In any case, I'm not taking the absolute number as > quite so important as the general sense of being able to search over > "all" the free sources. (There is a fee for using CWM GlobalSearch > beyond the trial period, but at EUR 120 / year, this is pretty close > to "free".) > > Of course, there are a lot of excellent "for fee" sources out there > that one needs to consider when trying to do a comprehensive search. > But for certain types of searches ("where can I get this?" "has this > already been reported?" "who else is working on this?" "how has this > been commonly used?"), this is an excellent place to start. > > Cheers, > David > > > From: owner-chemistry%x%ccl.net [mailto:owner-chemistry%x%ccl.net] > Sent: Friday, May 09, 2008 1:35 AM > Subject: CCL: New software for searching the web for chemical > information > > David, > I took an early look at this application and was asked whether we were > okay with having ChemSpider as part of the search and I of course > agreed in keeping with our recent Creative Commons announcement.here > http://www.chemspider.com/blog/chemspider-adopts-creative-commons-licenses.html. > > As a user of the system I am interested in your experiences relative > to the online services such as ChemSpider, PubChem or the Chemical > Structure Lookup Service. What are the advantages > from your point of > view (please feel free to connect with me offline). > > One comment, and I am sure that people are aware of it, is that the > advertised 100 million structures are of course not unique structures. > The PubChem dataset is on ChemSpider and ChemSpider is on PubChem > (http://www.chemspider.com/blog/pubchem-deposition-of-chemspider-data-is-well-underway-my-favorite-color-is-green.html). There is a lvery large amount of overlap between all of the datasets and I based on experience I would estimate the number of unique structures at around 25-30 million. Do you happen to know what the real number of unique structures is? > > Best wishes > > PS. There was an interesting article about ChemSpider published in > Nature yesterday – these systems of "global chemistry searching" are > growing in number. > http://www.chemspider.com/blog/nature-writes-about-chemspider.html > > > Antony Williams, > URL: www.chemspider.com > Email: antony.williams-*-chemspider.com > Phone: (919) 341-8375 > Mobile: (919) 201-1516 > Fax: (919) 300-5321 > > CONFIDENTIALITY NOTICE > Unless expressly stated otherwise, this message is confidential and is > intended for the addressee(s) only. > If you are not an addressee, please inform the sender immediately or > contact feedback-*-chemspider.com. > > > From: owner-chemistry-*-ccl.net [mailto:owner-chemistry-*-ccl.net] > Sent: Thursday, May 08, 2008 9:33 AM > To: Antony Williams > Subject: CCL: New software for searching the web for chemical > information > > A friend recently showed me an interesting chemistry application that > I thought members of CCL would like to know about. This application > searches over "all" chemical information that is freely-available on > the web, including the internet itself, using a single search. It is > quite easy to use -- you simply draw a chemical structure, and start a > search. You can also use SDfiles to submit a series of compounds as > separate queries, simplifying searches for starting materials or test > compounds. > > The application is called "CWM Global Search". You can find > information about it at http://www.akosgmbh.de/globalsearch/index.htm, > including a movie showing the use of Global Search. I note that you > can now use this application for free for 7 days -- a convenient way > to see if it would be helpful to you. > > Cheers, > David > > David Hughes > Basel, Switzerland > > (Apologies for "cross-posting", but I really think this is useful > software to consider.)