From owner-chemistry@ccl.net Fri Apr 17 00:18:01 2009 From: "Kalju Kahn kalju|*|chem.ucsb.edu" To: CCL Subject: CCL: Optimization at MP4 level of the theory Message-Id: <-39096-090416233403-456-X2svAH0W6FU6r2ASotQkdw#server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 16 Apr 2009 20:33:42 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju- -chem.ucsb.edu] >> Sent to CCL by: "Syed Tarique Moin" [tarisyed,yahoo.com] >> Dear CCl users, >> >> I m optimizing the carbon, hydrogen and oxygen containing cluster >> compounds. at the MP4 level of the theory using DZP basis set.... > > Is this wise? Numerical optimisation with MP4 will take an enormous > amount of time. And the DZP basis set is not really a good match for MP4. To describe properly fourth-order electron correlation, one would need a basis with higher polarization functions. There are certain combinations of electron correlation and basis sets that are known to produce fairly accurate geometries, e.g. MP2/cc-pVTZ (see Exact Geometries from Quantum Chemical Investigations by D. Cremer, E. Kraka, and Y. He in J. Mol. Structure, 567-568, 275-293 (2001)). A combination of high-order MP methods with small basis set could lead to nonsense: CO2 dissociates at MP6/cc-pVDZ! Numeric optimization of highly symmetric molecules with such large basis at MP4 is feasible, but once the number of symmetry-independent variables gets larger, computational time becomes prohibitive. My two cents, Kalju ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Fri Apr 17 09:18:01 2009 From: "Andreas Klamt klamt|*|cosmologic.de" To: CCL Subject: CCL: Presentation at COSMO-RS Symposium 2009 Message-Id: <-39097-090417091242-15246-B4jnB1a3r92AZNFFflyiRw#,#server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 17 Apr 2009 15:12:26 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt-$-cosmologic.de] Dear CCLers, two weeks ago we held the COSMO-RS Symposium 2009 on the occasion of our 10th company anniversary. Maybe that some of you like to have a look at the presentations. The COSMO-RS Symposium really was a great success. We had about 100 participants from academia and industry from all over the world. In 30 oral presentations and 23 posters the symposium a great variety of different COSMO-RS applications and related aspects have been presented by experienced users. Many of the presentations are now available for download on our website http://www.cosmologic.de. You will also find a foto gallery, reflecting the excellent conference atmosphere in the wonderful conference hotel Maria in der Aue. Thanks again to all participants, who contributed to the success of the meeting by presentations, intensive discussions, and by networking on future applications. Best regards and maybe see you at the next COSMO-RS Symposium in about 2.5 years Andreas Klamt -- -------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt|a|cosmologic.de web: www.cosmologic.de -------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics -------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri Apr 17 10:31:01 2009 From: "Jim Kress ccl_nospam-$-kressworks.com" To: CCL Subject: CCL: chemcraft, cubegen and density Message-Id: <-39098-090415231226-24385-W2OYbZhCPGGDsppjaLWivg/a\server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 15 Apr 2009 23:07:22 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam|a|kressworks.com] Chemcraft (and most other programs that render molecular density) only render the density for an isosurface of a specific value. In Chemcraft = you can change the value of the isosurface you wish to visualize, use the = Style function to make it transparent and then hit the "Keep this surface" = button. Then, change the Contour value to a different value, use the Style = function to make it a different color, and then "Keep this surface". You can do = this for as many surfaces as you want. However, the graphics of your system = will become overwhelmed after more than 10 isosurfaces (at least for larger = (>20 atoms) systems. Good luck. You might also want to try OpenDX. It does true 3D rendering (not just isosurfaces) but it's a pain in the ass to learn. Jim > -----Original Message----- > From: owner-chemistry+ccl_nospam=3D=3Dkressworks.com]*[ccl.net=20 > [mailto:owner-chemistry+ccl_nospam=3D=3Dkressworks.com]*[ccl.net]=20 > On Behalf Of Madi madi7sk]^[gmail.com > Sent: Sunday, April 12, 2009 4:52 PM > To: Kress, Jim > Subject: CCL: chemcraft, cubegen and density >=20 >=20 > Sent to CCL by: Madi [madi7sk]*[gmail.com] Hi David, >=20 > It says "Electron density from Total SCF Density" on the left=20 > work area. > Is there a command line that i need to use during the making=20 > of cube file to get "electron density from spin"?. I tried=20 > changing the contour value to 0.0008. the blob gets much=20 > bigger. when I go to higher contour values, size of the blobs=20 > become smaller. The blob stays in single colour though. > There are other parameters such as values range and scale. =20 > Are there appropriate settings for those that i need to use? >=20 > Thank you for your help > Madi >=20 > On Sun, Apr 12, 2009 at 2:22 PM, Close, David M.=20 > CLOSED##mail.etsu.edu wrote: > > > > Sent to CCL by: "Close, David M." [CLOSED(0)mail.etsu.edu] > > Madi: > > =A0When you open the .cube file, does a work area appear on=20 > the left that says "Electron Density from Spin" ? =A0If so,=20 > move down to the choice "Show Isosurface, and then click on=20 > the "Both Signed" option to the right. =A0You still may not see=20 > what you want because the Contour Value is too big. =A0Click on=20 > the Contour Value to make it below say 0.0008, and you should=20 > see positive and negative spin densities. > > =A0Regards, Dave Close. > > > > -----Original Message----- > >> From: owner-chemistry+closed=3D=3Detsu.edu**ccl.net=20 > >> [mailto:owner-chemistry+closed=3D=3Detsu.edu**ccl.net] On=20 > Behalf Of Madi=20 > >> madi7sk _ gmail.com > > Sent: Saturday, April 11, 2009 11:38 AM > > To: Close, David M. > > Subject: CCL: chemcraft, cubegen and density > > > > > > Sent to CCL by: Madi [madi7sk-.-gmail.com] Hi All I am=20 > sorry about not=20 > > wording the question properly. > > I meant to ask how to see regions of high and low electron=20 > densities. > > Right now i am able to see only one colored blob on the molecule. > > > > Thanks > > madi > > On Sat, Apr 11, 2009 at 9:53 AM, Madhavan Narayanan=20 > > madi7sk_._gmail.com wrote: > >> > >> Sent to CCL by: "Madhavan =A0Narayanan" [madi7sk * gmail.com] Hi, > >> > >> I converted my check point file to .fchk and then to .cube. > >> Then I tried opening it in chemcraft. When I opened it to=20 > view the electron density, I see only atoms with positive=20 > density. How do I get it to show me both positive and=20 > negative regions? I am very new to this and would appreciate any help. > >> > >> Thank you > >> Madi > >> > >> > >> > >> -=3D This is automatically added to each message by the=20 > mailing script=20 > >> =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> = =A0 =A0 =A0> =A0 =A0 =A0> =A0 =A0 =A0> > >> > >> > > > > > > > > -- > > > > > > > > -=3Dhis is automatically added to each message by the mailing script = > > =3Dhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messageJob:=20 > > http://www.ccl.net/jobs> > > > > - This is automatically added to each message by the=20 > mailing script -> =A0 =A0 =A0> =A0 =A0 =A0> =A0 =A0 =A0> =A0 =A0 =A0> > > > > >=20 >=20 >=20 > -=3Dhis is automatically added to each message by the mailing=20 > script =3D To recover the email address of the author of the=20 > message, please change the strange characters on the top line=20 > to the ]*[ sign. You can also look up the X-Original-From: line=20 > in the mail header. >=20>=20>=20 > Subscribe/Unsubscribe:=20>=20>=20> Conferences:=20 > http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20>=20>=20 >=20 From owner-chemistry@ccl.net Fri Apr 17 11:16:00 2009 From: "Henry Martinez hmartine%%gmail.com" To: CCL Subject: CCL:G: Coupling constants with Gaussian Message-Id: <-39099-090417111404-2572-GFR7IfsmgSo561jOhS5xdg=-=server.ccl.net> X-Original-From: "Henry Martinez" Date: Fri, 17 Apr 2009 11:14:00 -0400 Sent to CCL by: "Henry Martinez" [hmartine-x-gmail.com] Hi, I am using Gaussian 03 to find some coupling constants; however, I am using very large structures, and I just need the coupling constants of 3 specific atoms, so, I would like to know if any of you know the keyword, and where and how to put it in Gaussian, in order to calculate just the coupling constant of the atoms I need and do the calculation much faster. I know is possible, I just do not know how. Thanks a lot From owner-chemistry@ccl.net Fri Apr 17 11:53:01 2009 From: "Kenny Bravo kenny++fq.uh.cu" To: CCL Subject: CCL: Dalton 2.0 Message-Id: <-39100-090417102943-13776-yMrb+8NexAltLQVtnXpigA^^server.ccl.net> X-Original-From: "Kenny Bravo" Date: Fri, 17 Apr 2009 10:29:39 -0400 Sent to CCL by: "Kenny Bravo" [kenny[-]fq.uh.cu] Hello I want to perform a constrained geometry optimization using Dalton 2.0. I used .FINDRE to identify the redundant coordinate but the angle I want to keep fixed it is not included in the list of redundant internal coordinates. What can i do? Thanks in advanced From owner-chemistry@ccl.net Fri Apr 17 12:55:01 2009 From: "Elaine Meng meng(!)cgl.ucsf.edu" To: CCL Subject: CCL:G: density display, isosurfaces Message-Id: <-39101-090417121843-14702-70BBs2rRWWfr8XfrM1JYMw_-_server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 17 Apr 2009 12:18:39 -0400 Sent to CCL by: "Elaine Meng" [meng(a)cgl.ucsf.edu] Hello, In Chimera, it is fairly easy to display multiple isosurfaces of various colors. The density values are shown in a histogram, and a slider on the histogram sets the isosurface level. You can add more sliders just by Ctrl-clicking on the histogram, and of course you can move them around and change their colors. Of course, you would need to have the density in a format that Chimera knows -- Gaussian cube grid (.cube), gOpenMol grid (.plt), many others: Opening the file will bring up the Volume Viewer dialog for controlling the display. Here's a tutorial that includes displaying two isosurfaces of different colors. It uses X-ray crystallographic density, but the principles are the same: Best, Elaine ----- Elaine C. Meng, Ph.D. meng,,cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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 Fri Apr 17 13:30:01 2009 From: "Henry Martinez hmartine---gmail.com" To: CCL Subject: CCL: Dalton installation on MAC Message-Id: <-39102-090417130919-9206-jbP6fTte9h0bTMdhUivkUQ-$-server.ccl.net> X-Original-From: "Henry Martinez" Date: Fri, 17 Apr 2009 13:09:14 -0400 Sent to CCL by: "Henry Martinez" [hmartine[A]gmail.com] Hi, I would like to use Dalton on my MAC computer, but honestly I do not have a single idea how to do it. Would any one please tell me step by step how to do it. I have install the last MAC operative system. Thanks a lot From owner-chemistry@ccl.net Fri Apr 17 14:37:00 2009 From: "reynier.suardiaz.:.uam.es" To: CCL Subject: CCL: Coupling constants with Gaussian Message-Id: <-39103-090417142417-24589-Jw17QOU1RiSfNmdS5aG23w]*[server.ccl.net> X-Original-From: reynier.suardiaz[-]uam.es Date: Fri, 17 Apr 2009 18:37:50 MET Sent to CCL by: reynier.suardiaz++uam.es Hi Henry, Did you try nmr=readatoms? Other way is with IOp(10/48=10). This is an example for CH4 computing only 2JH2H3 ------------------------------------ %chk=ejemplo_ch4.chk %mem=60MW # nmr=spin IOp(10/48=10) B3LYP TZVP Title Card Required 0 1 C H 1 B1 H 1 B2 2 A1 H 1 B3 3 A2 2 D1 H 1 B4 3 A3 2 D2 B1 1.07000000 B2 1.07000000 B3 1.07000000 B4 1.07000000 A1 109.47120255 A2 109.47125080 A3 109.47121829 D1 -119.99998525 D2 120.00000060 2,3 --------------------------------- of course you should take into consideration the level of theory for your large structures etc, etc. Best reynier -------------------------------------------------------------------------- Mensaje enviado mediante una herramienta Webmail integrada en *El Rincon*: ------------->>>>>>>> https://rincon.uam.es <<<<<<<<-------------- From owner-chemistry@ccl.net Fri Apr 17 15:11:01 2009 From: "David Santos david++fq.uh.cu" To: CCL Subject: CCL: structure from hkl Miller index Message-Id: <-39104-090417140443-14378-d3jRwebDKMPwr3DYJMgDWQ**server.ccl.net> X-Original-From: "David Santos" Date: Fri, 17 Apr 2009 14:04:39 -0400 Sent to CCL by: "David Santos" [david::fq.uh.cu] Is there any (free) software that propose the structure of a solid from the hkl Miller index obtained from X-ray diffraction? Actually I want to know the parameters of the atoms in the unit cell for a salt of known molecular formula. I accept any other sugerence. Thanks in advance, David Santos Carballal Departamento de Qumica-Fsica Facultad de Qumica-Universidad de la Habana. Zapata s/n entre G y Carlitos Aguirre. Prncipe. Plaza de la Revolucin. Cdigo Postal 10400. Cuba e-mail: david|*|fq.uh.cu phone: 878-0684 url: http://www.fq.uh.cu/investig/gqf/e/dsc.htm From owner-chemistry@ccl.net Fri Apr 17 15:48:01 2009 From: "Yong Yan yyan(-)tulane.edu" To: CCL Subject: CCL: Webmo Kills my jobs every six hours Message-Id: <-39105-090417151103-13400-GdSaKIKxV14bemziIfyCTA!=!server.ccl.net> X-Original-From: "Yong Yan" Date: Fri, 17 Apr 2009 15:10:59 -0400 Sent to CCL by: "Yong Yan" [yyan!A!tulane.edu] Hi, All; I used the webmo with the account by my university (Tulane university). In previous days, everything goes on pretty well, but I do not know why in recent days, they are going to kill my jobs every six hours, no matter what job it is. Did anyone has the similar experience before? How can I improve it. Thank you very much! Best Wishes! Yong Yan yyan:_:tulane.edu From owner-chemistry@ccl.net Fri Apr 17 16:22:01 2009 From: "Ardie Putao cclreading.\a/.googlemail.com" To: CCL Subject: CCL:G: about the units of charge in G03 input file Message-Id: <-39106-090417143707-29264-WH5Ot1LEgx23bcA5RJ0LNw\a/server.ccl.net> X-Original-From: "Ardie Putao" Date: Fri, 17 Apr 2009 14:37:03 -0400 Sent to CCL by: "Ardie Putao" [cclreading#googlemail.com] Dear all, I want to take the point charge from TURBOMOLE's pointcharge file and add these charge data below the molecular coordinates line in a G03 input file to do a single point calculation. I know the default unit of the coordinates of background charge in TURBOMOLE is Bohr. But I checked the G03's manual and found it can also has the alter unit of Bohr although the default is angstrom. So I set the G03 input file as: # b3lyp/6-31g charge(Bohrs) test 0 1 N 0.445374 1.948804 0.851080 N 2.304173 0.138927 -0.418478 C 1.205959 -2.365229 -1.625987 C 0.683222 -3.540489 -2.312410 C -0.685657 -3.474430 -2.213680 C -0.984818 -2.255557 -1.479363 C -2.623677 -0.704717 -0.394601 C -3.984811 -0.373558 0.012206 C -3.891885 0.751463 0.810180 ... -6.2039726363 -66.7167998552 -23.3778085543 -0.3000000000 -6.1850753697 -68.5573936255 -22.7088453154 0.3300000000 -8.0559047665 -66.1328743162 -23.7406360737 0.3300000000 -5.5180018575 -65.4903672506 -21.9888594566 0.3300000000 -4.7186474788 -66.3672004225 -25.7494155170 0.2100000000 -2.7363242088 -66.5750703555 -25.3015502977 0.1000000000 -5.4707586909 -68.3419647859 -27.7506360536 0.1400000000 -5.2213147713 -70.2808243426 -26.9607303083 0.0900000000 -3.8550423936 -68.1076386796 -29.9143730834 -0.6600000000 -4.5447926257 -69.1545472512 -31.2466303811 0.4300000000 -8.2259801663 -67.9715783598 -28.5443212523 -0.2700000000 -8.7740008987 -69.4587932440 -29.9276011700 0.0900000000 -9.5620169174 -68.0963003196 -26.9380535883 0.0900000000 -8.5151083458 -66.1234256829 -29.5118613040 0.0900000000 -5.0909236315 -63.7178036402 -26.8700234285 0.5100000000 -6.9409660351 -62.4157819691 -26.2917670694 -0.5100000000 .. But the job stopped with the errors that G03 can not recognize the keyword bohrs. It seems that the Units(AU) does not work either. Because in G03 manual it says: the Charge, Cube and Massage keywords are not affected by the setting of the Units keyword, and their input is always interpreted in units of Angstroms and degrees. So, does anyone know how to do this single point without changing the coordinate of background charge from Bohrs to Angstroms? Any suggestion is appreciated. Thanks. Ardie From owner-chemistry@ccl.net Fri Apr 17 19:31:00 2009 From: "Elaine Meng meng]|[cgl.ucsf.edu" To: CCL Subject: CCL: Monitors for CADD/molecular modelling Message-Id: <-39107-090417192954-30223-E6crDHqgNHE/cWGbsuUmzQ*_*server.ccl.net> X-Original-From: "Elaine Meng" Date: Fri, 17 Apr 2009 19:29:50 -0400 Sent to CCL by: "Elaine Meng" [meng^cgl.ucsf.edu] Hi David, I know it's been a while since your question to CCL, but I wanted to note that recent daily builds of Chimera also support row-interleaved stereo: http://www.cgl.ucsf.edu/chimera/ Our lab has a Miracube LCD display for this type of stereo, discussed here: http://www.cgl.ucsf.edu/Outreach/technotes/miracube.html but we also have users with a Zalman monitor, mentioned in other responses to your question. The super-economy approach is to use red-cyan stereo (another Chimera option) with just about any old display and those very cheap cardboard/plastic glasses, but that only works well with colors that are not mostly red or mostly cyan, and probably would be hard to tolerate if used constantly. Best, Elaine ----- Elaine C. Meng, Ph.D. meng|-|cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) 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 Fri Apr 17 20:27:00 2009 From: "Venable, Richard (NIH/NHLBI) E venabler _ nhlbi.nih.gov" To: CCL Subject: CCL: Monitors for CADD/molecular modelling Message-Id: <-39108-090417202354-25419-nAxgjRwRFgqwAVWT8rYd0Q%%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: Fri, 17 Apr 2009 20:23:36 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler.:.nhlbi.nih.gov] Related to that, is anyone aware of a good source of stereoscopes? I'd fou= nd some sources of lightweight, inexpensive, handheld versions years ago fr= om a German company called VCH, and they were ideal for viewing side-by-sid= e stereo images, either printed or on the display screen. I can't seem to = find this companyany more, however, and I'd be interested in knowing of any= sources for these simple but useful devices. It's all done with mirrors, = they say ... :) Regards, -- Rick Venable 5635FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 4/17/09 7:29 PM, "Elaine Meng meng]|[cgl.ucsf.edu" wrote: Sent to CCL by: "Elaine Meng" [meng^cgl.ucsf.edu] Hi David, I know it's been a while since your question to CCL, but I wanted to note t= hat recent daily builds of Chimera also support row-interleaved stereo: http://www.cgl.ucsf.edu/chimera/ Our lab has a Miracube LCD display for this type of stereo, discussed here: http://www.cgl.ucsf.edu/Outreach/technotes/miracube.html but we also have users with a Zalman monitor, mentioned in other responses = to your question. The super-economy approach is to use red-cyan stereo (another Chimera optio= n) with just about any old display and those very cheap cardboard/plastic g= lasses, but that only works well with colors that are not mostly red or mos= tly cyan, and probably would be hard to tolerate if used constantly. Best, Elaine ----- Elaine C. Meng, Ph.D. meng##cgl.ucsf.edu UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html