From chemistry-request@server.ccl.net Tue Apr 23 04:13:24 2002 Received: from lgdx04.lg.ehu.es ([158.227.1.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3N8DMA31847 for ; Tue, 23 Apr 2002 04:13:23 -0400 Received: by lgdx04.lg.ehu.es id KAA0000022663; Tue, 23 Apr 2002 10:12:48 +0200 (MET DST) Message-ID: <009301c1ea9d$e37d76a0$222fe39e@lc.ehu.es> From: "Pablo Vitoria" To: "Harald Bock" , References: <200204142250.g3EMouHB018973@mail1.rrz.Uni-Koeln.DE> Subject: Re: CCL:ToPMod: have questions and need a little help! Date: Tue, 23 Apr 2002 10:07:18 +0200 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-15" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Hi Harald, I started recently using TopMoD, and since I have been a user of Molekel for a while now, I am using it to visualize the ELF basins. First, I generate the compid_elf.sbf file with top_grid (using a coarse grid, otherwise the final cube file may be quite large), and compid_ebas.sbf with top_bas (compid=name of the compound). If simmetry is used in top_grid, run top_sym on both compid_elf.sbf and compid_ebas.sbf. Then, run bas_to_syn, which will generate compid_esyn.sbf. To get the Gaussian cube files (to be used as input to Mlekel) of both compid_elf.sbf and compid_esyn.sbf, run sbf_to_cube with them as input files, to generate compid_elf.cube and compid_esyn.cube. In Molekel, load (as Gaussian cube) compid_elf.cube. This will only get the coordinates of your molecule, that will be visible now in the window. From the Surface menu, Load (Gaussian cube) compid_elf.cube, and Create Surface choosing an appropriate cutoff (usually between 0.7 and 0.8). You will see now all the basins with the same color. Load (Gaussian cube) compid_esyn.cube. Choose Grid Value button (to map the syn cube on the elf cube), and on the window that shows up, choose 1.0 as Vmax and 5.0 as Vmin (they seem to be reversed, at least in my version of Molekel). And you should see now the basins colored according to their type (core, monosynaptic, disynaptic,...). If you don´t like the default colors, you can change them in the Texture menu. I hope this helps you. Best regards Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Química Inorgánica, Facultad de Ciencias Universidad del País Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6012579 Fax. 94 4648500 ----- Original Message ----- From: "Harald Bock" To: Sent: Monday, April 15, 2002 2:02 AM Subject: CCL:ToPMod: have questions and need a little help! | Ladies and Gentlemen, | has anyone experience with the program-package ToPMod of Silvi et al. for | calculating ELF? | I've got everything set up and running, but I'm in need of some help with | visualisation of the output. | I would like to use Molekel but didn't succeed in assigning different colors | to the different basins types by using bat_to_syn due to a lack of | documentation (if it is possible at all). | | If there is anyone out there, able and willing to help me, I would be very | thankfull. | Harald Bock | University of Cologne | | | -= This is automatically added to each message by mailing script =- | CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins | MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH | CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 | Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net | | | | | | From chemistry-request@server.ccl.net Tue Apr 23 09:21:12 2002 Received: from prserv.net ([32.97.166.32]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3NDLBA04201 for ; Tue, 23 Apr 2002 09:21:11 -0400 Received: from attglobal.net (slip-32-101-104-225.in.us.prserv.net[32.101.104.225]) by prserv.net (out2) with SMTP id <2002042313210120204d6i4ce>; Tue, 23 Apr 2002 13:21:04 +0000 Message-ID: <3CC5194B.DB2C29F3@attglobal.net> Date: Tue, 23 Apr 2002 08:20:27 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: h9531257 CC: CHEMISTRY@ccl.net Subject: Re: CCL:Program to resolve colse peaks References: <3CD02D0A@webmailb.hku.hk> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have had very good luck with PeakFit from SPSS. It's not free, but has good graphics, and many fitting functions built in, and is fast. John McKelvey h9531257 wrote: > Dear all, > > Does anyone know that is there any program that can be used to resolve very > close absorption peaks? Say, the splitting of a very board absorption peak? > > The oscialltor strength and peak energy could be roughly be estimated as the > input information. > > Thanks anyone who can help. > > Andy > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net From chemistry-request@server.ccl.net Tue Apr 23 10:21:20 2002 Received: from web12805.mail.yahoo.com ([216.136.174.40]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g3NELJA05446 for ; Tue, 23 Apr 2002 10:21:19 -0400 Message-ID: <20020423142106.56245.qmail@web12805.mail.yahoo.com> Received: from [203.87.132.164] by web12805.mail.yahoo.com via HTTP; Tue, 23 Apr 2002 07:21:06 PDT Date: Tue, 23 Apr 2002 07:21:06 -0700 (PDT) From: amor san juan Subject: Data for testing AutoDock3 To: chemistry@ccl.net Cc: garrett@scripps.edu MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Dear CCLers; I successfully compiled AutoDock 3 (AD3) in Red Hat 7 linux platform. My goal now is to test this using already established data in AD3. Would anyone please send me tar zipped file of ligand+enzyme where I can check if my compilation are all correct. There is 3PTB file in AutoDock website used in testing only compilation of AutoDock2.4. I need file data used to test AD3. To give time & effort in replying to this message means a lot to me, hoping anyone out there again will give me this favor. Amor San Juan University of the Philippines-Diliman __________________________________________________ Do You Yahoo!? Yahoo! Games - play chess, backgammon, pool and more http://games.yahoo.com/ From chemistry-request@server.ccl.net Tue Apr 23 12:20:28 2002 Received: from sagres.tcc (user@[193.137.208.70]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3NGKSA07750 for ; Tue, 23 Apr 2002 12:20:28 -0400 Received: from ci.uc.pt (localhost.localdomain [127.0.0.1]) by sagres.tcc (8.11.6/8.11.6) with ESMTP id g3NGXvW31095 for ; Tue, 23 Apr 2002 17:33:57 +0100 Sender: jorge@sagres.tcc Message-ID: <3CC58CF5.38CE634B@ci.uc.pt> Date: Tue, 23 Apr 2002 17:33:57 +0100 From: Jorge Manuel Campos Marques X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.9-31 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Summary about "Complex matrix diagonalization routine" Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear CCLers, About two months ago I asked for a complex matrix diagonalization routine. I would like to thank all those who kindly gave any information or suggestion. I apologize for this so late email and summarize here all the answers to my question: ----------------------------------------------------------------------------------------- Dear cclers, We need a complex matrix diagonalization routine in fortran 77. We have already tried one from EISPACK called CG.F, but it does not work very well. Could you kindly tell me another one? Thanking in advance J. Marques -------------------------------------------------------------- Hi Jorge, try www.netlib.org/lapack and the subroutines therein. You will need to specify complex/double complex. Good luck, Thomas ------------------------------------------------------------- Dear Jorge, I guess you can find what you are looking for in the free lapack library available from netlib. However, if you are looking specifically for complex-symmetric matrices (i.e., A(i,j) = A(j,i)) you can find very efficient code at: http://www.technion.ac.il/technion/chemistry/cc/sw/ Regards, Thomas --------------------------------------------------------------- Robert L Waterland wrote: I have had excellent results with the routines in LAPACK. You didn't specify if you wanted eigenvalues only or eigenvalues and eigenvectors. The driver routine for all eigenvalues and eigenvectors of a single precision complex Hermitian matrix is called CHEEV. Routines for all the common matrix types are in LAPACK. You can get the routines and descriptions from www.netlib.org. I'm surprised you had problems with a routine from EISPACK -- what was happening? ---------------------------------------------------------------- Miroslava Cuperlovic-Culf wrote: There are other subroutines in eispek and linpak. One that we used is subroutine eisdia. We used it for density matrix diagonalization and it worked well for at least 2Kx2K matrices. It needs some other subroutines available from the same place. I am sending to you whole file that we used for matrix manipulation (with eisdia and everything else). Mira ---------------------------------------------------------------- Konrad Hinsen wrote: The state of the art for almost everything in linear algebra is LAPACK, available from www.netlib.org (and others). ----------------------------------------------------------------- Is there not one called CH ? Best regards, Trond SAUE ----------------------------------------------------------------- zdenko tomasic wrote: check LAPACK library from netlib for dense matrices or ARPACK from the same place for sparse ones ----------------------------------------------------------------- Christoph van Wüllen wrote: I once used a routine from the "Numerical Recipes" Book, and it worked. I also have tested a complex Jacobi routine, but this was slower. So look in "numerical recipes", this advice applies also in other situations. ----------------------------------------------------------------- From chemistry-request@server.ccl.net Tue Apr 23 11:57:03 2002 Received: from hotmail.com ([64.4.9.46]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3NFv3A07453 for ; Tue, 23 Apr 2002 11:57:03 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Tue, 23 Apr 2002 08:56:52 -0700 Received: from 63.184.71.13 by lw9fd.law9.hotmail.msn.com with HTTP; Tue, 23 Apr 2002 15:56:51 GMT X-Originating-IP: [63.184.71.13] From: "Fernando De La Vega" To: CHEMISTRY@ccl.net Subject: Summary: Gaussian98 Warning Message Date: Tue, 23 Apr 2002 08:56:51 -0700 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 23 Apr 2002 15:56:52.0535 (UTC) FILETIME=[7C321C70:01C1EADF] Dear All, Last week I asked a question with regard to the warning received in Gaussian98 that reads: "Warning!!: The largest alpha MO coefficient is #########", where the #'s represent a given (usually large) number. I want to thank Douglas Fox (from Gaussian Tech Support), Antonio Marquez and Christoph van Wüllen for their response to my inquiry. Below I reproduced their answers. ---------------------------------------------------- Douglas J. Fox: Fernando, The warning is most relevant for post-HF calculations like Moller Plesset perturbation theory or coupled cluster, where the accuracy of the result is related to the accuracy of the MO integrals. When you have near linear dependencies in the basis set you will get large MO coefficients related to maintaining orthogonality. The side effect of large coefficients is loss of precision on any existing machine. Depending on the order that you add C1*I1+C2*I2-C3*I3+C4*I4 where C1 and C3 are large and of the same sign, if the integrals are all about the same size and C1*I1-C3*I3 is near zero the contribution from C2 or C4 can be lost if they are added before C3 is subtracted. For HF and DFT calculations the code which checks this is run but seldom is it an issue, it is actually just after the SCF completes. For any post-HF method look to see that the correlation corrections are a moderate fraction of the total energy. It may not be an error but it is worth comparing with a slightly smaller basis or a different correlation method, CCSD is less sensitive than MP4, as a check. --------------------------------------------------------------- Antonio Marquez (marquez@us.es): Dear Fernando, I guess that you mean that ####### is a LARGE number. This means that you have a nearly linearly dependent AO basis set. The closer you are to have a really linearly dependent basis set the biggest will be the number. For HF calculations this is not usually a problem as the large number(s) is(are) in one (or more) of the virtual MO that are just the orthogonal complement to your occupied MO. Problems may arise if these orbitals are used for a subsequent correlated ab initio calculation. During the 2e-integrals transformation to the MO basis the AO integrals will be mutiplied by the all the MO coefficients. If one or more of your coefficients if very high the numerical precision on your transformed MO integrals will be compromised and you have to be carefull with the result. The ways to circumvent this problem are either reduce the linear dependency in your AO basis set or use an algorithm to compute the 2e repulsion integrals that mantains a high degree of numerical accuracy. I hope this clarifies a little bit your doubts. ---------------------------------------------------------------- Christoph van Wüllen (Christoph.vanWullen@TU-Berlin.De): This means that you have a near-linear-dependency in your basis sets, e.g. if you have diffuse functions on two atoms which are quite close. Since very similar wavefunctions can result from very different coefficients, numerical problems might arise in force constant or correlation calculations. If you are sure that there is no input error, proceed (with care). ----------------------------------------------------------- _________________________________________________________________ MSN Photos is the easiest way to share and print your photos: http://photos.msn.com/support/worldwide.aspx From chemistry-request@server.ccl.net Tue Apr 23 23:24:18 2002 Received: from mail.chem.tamu.edu ([165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g3O3OIA17573 for ; Tue, 23 Apr 2002 23:24:18 -0400 Received: from [165.91.177.32] (account yubofan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5.2) with ESMTP id 1427027 for CHEMISTRY@ccl.net; Tue, 23 Apr 2002 21:24:14 -0600 Sender: yubo@ccl.net Message-ID: <3CC625CD.68BBC46B@mail.chem.tamu.edu> Date: Tue, 23 Apr 2002 22:26:06 -0500 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: NLMO Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id g3O3OIA17574 Hi, I tried to analyze localized orbital situation for one transition state but failed. The input file is: ================================================================ %nproc=1 %mem=64MB %chk=ts.chk #P B3LYP/GEN PSEUDO=Cards GEOM=Check GUESS=Read POP=NBORead TS 0 1 Basis Sets and ECP $NBO BNDIDX NLMO $END ================================================================ The error message in the output file is: ================================================================ NATURAL LOCALIZED MOLECULAR ORBITAL (NLMO) ANALYSIS: Highest occupied NBOs are not at the beginning of the NBO list; The NLMO program is not currently set up to handle this. ================================================================ Any advice? Thanks in advance. Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================