From owner-chemistry@ccl.net Fri Jan 20 05:02:00 2006 From: "Egon Willighagen egonw_-_sci.kun.nl" To: CCL Subject: CCL: Command-line tools for converting chemical files into graphics files? Message-Id: <-30586-060120044332-4915-1GVZF2h8ZYMk/aluPRPKRQ/a\server.ccl.net> X-Original-From: Egon Willighagen Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" Date: Fri, 20 Jan 2006 10:42:39 +0100 MIME-Version: 1.0 Sent to CCL by: Egon Willighagen [egonw/a\sci.kun.nl] On Thursday 19 January 2006 22:43, Rajarshi Guha rxg218 : psu.edu wrote: > Sent to CCL by: Rajarshi Guha [rxg218[*]psu.edu] > On Thu, 2006-01-19 at 14:18 -0500, Egon Willighagen egonw===sci.kun.nl > > And what about converting a SDF into 2D graphics wrapped into a PDF? Are > > there free or open source tools for that too? > > The program is now updated to optionally produce PDF output. It needs > the iText library ( http://www.lowagie.com/iText/index.html ) to be in > the CLASSPATH. What I actually meant was one PDF with the molecules in a table, possibly with molecular properties (e.g. from the SDF) file in a second column. But starting from your source I was able to add this feature to your code, and will send a patch privately. > Latest version can be obtained from > http://blue.chem.psu.edu/~rajarshi/code/java/#draw2d I hope you can integrate it with your code. BTW, the java source does not state a license, but I assume it's open source, correct? Egon -- e.willighagen]*[science.ru.nl PhD student on Molecular Representation in Chemometrics Radboud University Nijmegen Blog: http://chem-bla-ics.blogspot.com/ http://www.cac.science.ru.nl/people/egonw/ GPG: 1024D/D6336BA6 From owner-chemistry@ccl.net Fri Jan 20 06:16:01 2006 From: "Jacco van de Streek streek,,ccdc.cam.ac.uk" To: CCL Subject: CCL: Synthesize X-ray pattern Message-Id: <-30587-060120061434-10072-JZnyi3qFLczR9KNSDtkp5A#server.ccl.net> X-Original-From: Jacco van de Streek Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 20 Jan 2006 10:18:15 +0000 MIME-Version: 1.0 Sent to CCL by: Jacco van de Streek [streek]|[ccdc.cam.ac.uk] Nuno R. L. Ferreira nunolf~!~ci.uc.pt wrote: > I'm looking for a free tool that syntesizes the X-ray pattern, given a > protein pdb file. Mercury can do this: http://www.ccdc.cam.ac.uk/products/csd_system/mercury/ Mercury is freely available for several platforms, e.g. Windows and Linux, and can read and write .pdb, .res, .mol, .mol2 and .cif files. The simulated powder diffraction patterns can be saved in a format that can be read into e.g. MS-Excel. I have never tested the speed of simulating a powder diffraction pattern of a protein, but on a modern computer this will not be an issue. Beware that there are several programs, both commercial and free, that have errors in their simulated X-ray powder diffraction patterns. This pertains for example to crystal structures in trigonal space groups and to crystal structures where the inversion centre is not at the origin. Mercury was written to be completely general and is well tested, and should not have any problems with these cases. .pdb files have an added complication: the space group is given by the space-group name, which is not unique. Space groups like Fddd and P212121 have several settings, which all have the same name. For space groups like this, a program that simulates powder diffraction patterns has to "guess" which of the settings was intended, which in practice means that these programs choose the standard setting from the International Tables, which may or may not be correct. If the .pdb file came from the PDB, the PDB may have rules that take care of this, but for most other purposes, it is better to switch to .cif (or mmCIF) or .res files, where the symmetry operators are given explicitly. Best wishes, -- Dr Jacco van de Streek Research Scientist Cambridge Crystallographic Data Centre Cambridge, United Kingdom From owner-chemistry@ccl.net Fri Jan 20 07:41:00 2006 From: "=?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= FB153746,,ATIL.CEA.FR" To: CCL Subject: CCL: RE : Synthesize X-ray pattern Message-Id: <-30588-060120073756-4011-V1O9Y1PfYFcjeju1tb3eSw*server.ccl.net> X-Original-From: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 20 Jan 2006 12:45:58 +0100 MIME-Version: 1.0 Sent to CCL by: =?iso-8859-1?Q?BOUYER_Fr=E9d=E9ric_153746?= [FB153746^ATIL.CEA.FR] I know both Mercury, and Xpow. Both do and compute XDR patterns very mell, and CORRECTLY !! Regards -----Message d'origine----- De : owner-chemistry===ccl.net [mailto:owner-chemistry===ccl.net] Envoyé : jeudi 19 janvier 2006 20:10 À : B, F Objet : CCL: Synthesize X-ray pattern Sent to CCL by: "Nuno R. L. Ferreira" [nunolf],[ci.uc.pt] Hi * I'm looking for a free tool that syntesizes the X-ray pattern, given a protein pdb file. Best regards, Nuno ###################################### Nuno Ricardo Santos Loureiro da Silva Ferreira Departamento de Química Faculdade de Ciências e Tecnologia Universidade de Coimbra 3004-535 Coimbra - Portugal Fax: +351 239 827703 - www.biolchem.qui.uc.pt ######################################## --- avast! Antivirus: Outbound message clean. Virus Database (VPS): 0603-3, 18-01-2006 Tested on: 19-01-2006 16:37:16 avast! - copyright (c) 1988-2005 ALWIL Software. http://www.avast.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Fri Jan 20 11:13:00 2006 From: "Georg Lefkidis lefkidis : physik.uni-kl.de" To: CCL Subject: CCL:G: Unpaired electrons (not high spin) Message-Id: <-30589-060120101024-9283-sY0f/B+VKit+lcn3g2/sLw|,|server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 20 Jan 2006 15:23:06 +0100 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis=-=physik.uni-kl.de] Hi, does anyone know whether it is possible to explicitely ask for unpaired alpha and beta electrons in Gaussian? I mean except CASSCF. Georg Lefkidis -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.375 / Virus Database: 267.14.21/235 - Release Date: 19/01/06 From owner-chemistry@ccl.net Fri Jan 20 11:47:01 2006 From: "Jens Spanget-Larsen spanget(!)ruc.dk" To: CCL Subject: CCL:G: Transition Dipole Moment with Gaussian. Message-Id: <-30590-060120113845-3193-Ts7fJkuPpuvMN/5OmZw3qw:-:server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 20 Jan 2006 16:37:43 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget .. ruc.dk] Dear Roman, include iop(7/33=1) with the freq keyword, and the job will output (a lot of) additional information, such as the dipole derivatives with respect to the x, y, and z components of the different normal modes. The orientation of the axes is that of the standard orientation. For example: # B3LYP/cc-pVTZ freq iop(7/33=1) Dipole derivatives wrt mode 1: 7.76256D-10 3.54506D-10 4.43357D-02 Dipole derivatives wrt mode 2: -4.76908D-10 -6.90744D-10 -4.46843D-01 Dipole derivatives wrt mode 3: -2.30953D-01 -5.61704D-01 1.38640D-10 etc. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget*_*ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Roman D. Gorbunov gorbunov]=[theochem.uni-frankfurt.de wrote: > Sent to CCL by: "Roman D. Gorbunov" [gorbunov%theochem.uni-frankfurt.de] > Dear All, > > I would like to calculate transition dipole moment of a molecule with the usage of Gaussian program. If Gaussian calculate normal modes, in the end of the output files one can find something like this: > > MSD=1.034e-09\RMSF=5.113e-05\Dipole=1.203046,-0.9454618,0.4733203\Dipo > leDeriv=0.3104709,0.0526555,-0.0901773,0.0975203,0.3147646,-0.1101542, > -0.1478299,-0.0861128,0.4431087,-1.1332275,0.0824717,0.2775604,0.07129 > > I supposed that numbers coming after DipoleDeriv are derivatives of the dipole moment over normal coordinates (i. e. transition dipole moments). I also supposed that they are given in the initial-orientation frame (just like the dipole moment vector coming right before). However, under this suppositions I cannot get expected results. Does anybody know the exact definition and printing format of the dipole derivatives tensor in Gaussian output files? Or may be where one can read about that? > > Thank you in advance. From owner-chemistry@ccl.net Fri Jan 20 12:22:00 2006 From: "Zeki Buyukmumcu zbmumcu!A!yahoo.com" To: CCL Subject: CCL: Vibrational spectra of polymers Message-Id: <-30591-060120114042-4032-A4LF5KN6L1W1waExyfCpww!=!server.ccl.net> X-Original-From: Zeki Buyukmumcu Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 20 Jan 2006 07:40:33 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Zeki Buyukmumcu [zbmumcu],[yahoo.com] Dear CCL People, I need a free software-program code to calculate vibrational spectrum of polymers. I would be glad if you could reply in the case that you know. best regards... __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Fri Jan 20 12:58:00 2006 From: "Abrash, Samuel sabrash]^[richmond.edu" To: CCL Subject: CCL:G: Unpaired electrons (not high spin) Message-Id: <-30592-060120113845-1234-rwbWIatBll1nH9WbQnS8bA]|[server.ccl.net> X-Original-From: "Abrash, Samuel" Date: Fri, 20 Jan 2006 11:51:35 -0500 Sent to CCL by: "Abrash, Samuel" [sabrash : richmond.edu] I think you just set the multiplicity to 3, i.e. in the line preceding the input geometry instead of 0 1, indicating a charge of 0 and a multiplicity of 1 you'd put 0 3 (charge 0, multiplicity of 3). Best, Sam -----Original Message----- From: Georg Lefkidis lefkidis : physik.uni-kl.de [mailto:owner-chemistry!=!ccl.net] Sent: Fri 1/20/2006 11:29 AM To: Abrash, Samuel Cc: Subject: CCL:G: Unpaired electrons (not high spin) Sent to CCL by: "Georg Lefkidis" [lefkidis=-=physik.uni-kl.de] Hi, does anyone know whether it is possible to explicitely ask for unpaired alpha and beta electrons in Gaussian? I mean except CASSCF. Georg Lefkidis -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.375 / Virus Database: 267.14.21/235 - Release Date: 19/01/06 From owner-chemistry@ccl.net Fri Jan 20 14:34:00 2006 From: "Dra. Silvina Pellegrinet pellegrinet,+,iquios.gov.ar" To: CCL Subject: CCL:G: gaussian error Message-Id: <-30593-060120140502-32688-A0j8IPdtf77aatQwlCZ01w() server.ccl.net> X-Original-From: "Dra. Silvina Pellegrinet" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset=iso-8859-1; reply-type=original Date: Fri, 20 Jan 2006 15:04:08 -0300 Mime-Version: 1.0 Sent to CCL by: "Dra. Silvina Pellegrinet" [pellegrinet!=!iquios.gov.ar] i'm trying to run a frequency calculation using Gaussian 98 for windows but the calculation fails to end normally, giving me the following message: Not enough memory in AlgDDF. Error termination via Lnk1e in C:\G98W\l1002.exe. I would appreciate if you could tell me how to solve this problem. Thank you in advance for your help. Silvina From owner-chemistry@ccl.net Fri Jan 20 15:09:00 2006 From: "Kirkpatrick, James james.kirkpatrick[#]imperial.ac.uk" To: CCL Subject: CCL:G: Unpaired electrons (not high spin) Message-Id: <-30594-060120125047-1234-0R3agrqJ/SLf/diR5qL7hg|server.ccl.net> X-Original-From: "Kirkpatrick, James" Date: Fri, 20 Jan 2006 17:46:42 -0000 Sent to CCL by: "Kirkpatrick, James" [james.kirkpatrick .. imperial.ac.uk] You should be able to choose the spin mulitplicity for a particular = charge to obtain an arbitrary number of unpaired spins using any method. = James -----Original Message----- From: Georg Lefkidis lefkidis : physik.uni-kl.de = [mailto:owner-chemistry!A!ccl.net] Sent: Fri 1/20/2006 4:17 PM To: Kirkpatrick, James Subject: CCL:G: Unpaired electrons (not high spin) =20 Sent to CCL by: "Georg Lefkidis" [lefkidis=3D-=3Dphysik.uni-kl.de] Hi, does anyone know whether it is possible to explicitely ask for unpaired alpha and beta electrons in Gaussian? I mean except CASSCF. Georg Lefkidis