From chemistry-request@server.ccl.net Fri Jul 23 16:41:03 1999 Received: from ibitipoca.fisica.ufjf.br (dantas@[200.17.69.110]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA15203 for ; Fri, 23 Jul 1999 16:40:53 -0400 Received: (from dantas@localhost) by ibitipoca.fisica.ufjf.br (8.8.7/8.8.7) id SAA03776; Fri, 23 Jul 1999 18:36:16 -0300 Date: Fri, 23 Jul 1999 18:36:16 -0300 From: Socrates de Oliveira Dantas Message-Id: <199907232136.SAA03776@ibitipoca.fisica.ufjf.br> To: chemistry@ccl.net Subject: Hello guys... Cc: have.csd@ibitipoca.fisica.ufjf.br I need your help! I am not a regular reader of this list, so if someone could help me with this topic please write direct to my e-mail address: dantas@fisica.ufjf.br I have the following problem i need to read a the atached file and translate it to a zmt or pdb file. i have tried Spartan, Babel, Hyperchem and no result at all. So do you guys know what kind of software or visualizer could i use to translate this file: (just after ####). Thanks in advance. Prof. Socrates de Oliveira Dantas #### #YIVLIY #ADATE 951127 #COMPND 9-(1,2,3,4-Tetrahydro-1-thiaphenanthren-4-ylidene)-2- dimethylamino-cis-7-nitro-10-thia-anthracene #QUAL at 130 deg.K. #FORMUL C28 H22 N2 O2 S2 #AUTHOR W.F.Jager,J.C.de Jong,B.de Lange,N.P.M.Huck,A.Meetsma, B.L.Feringa #JRNL 179,34,348,1995 #CREF nbsid 649094 batch 254 #SYSCAT sys A cat 3 #CONN El= N 24 26 O 30 31 S 14 22 V= 5 11 19 24 Res= Plot= 1 B= 1 1-3 1-4 2-5 2-6 6-13 7-14 9-14 12-22 13-22 16-24 18-26 26-32 26-33 B= 2 1-2 24-30 24-31 B= 5 3-7 3-8 4-9 4-10 5-11 5-12 7-15 8-16 9-17 10-18 11-19 11-20 12-21 15-23 16-23 17-25 18-25 19-27 19-28 20-29 21-27 28-34 29-34 #DIAGRAM 500 430 500 571 413 380 588 380 413 621 586 621 413 279 326 430 588 279 675 430 326 571 413 721 587 721 501 229 326 229 239 380 674 229 762 379 240 621 326 471 327 771 500 771 239 280 151 16430 761 279 849 23430 240 721 153 571 239 421 0 0 0 0 0 0 0 0 152 471 0 0 0 0 #CELL a 10.431 b 11.103 c 11.525 alpha 114.997 beta 106.01 gamma 94.078 z 2 sg P-1 cent 1 #SYMM x,y,z #DENSITY dx 1.411 #UNIS int 3 sigcc 1 #FLAGS err 0 #RFACT R= 0.0340 #PROPS "Mp. 212 deg.C "Color: red #RADIUS C 0.68 N 0.68 O 0.68 S 1.02 #TOLER 0.40 #ATOM S1 0.16180,6 1.13589,5 0.50960,6 S2 0.09462,6 0.41392,5 0.23131,5 O1 0.19105,19 0.89587,16 0.85567,17 O2 0.32294,17 0.76879,17 0.90204,16 N1 0.23985,19 0.79388,18 0.82140,18 N2 -0.33923,19 0.64633,18 -0.00957,19 C1 0.2896,2 1.0576,2 0.5645,2 C2 0.3905,2 1.1418,2 0.6928,2 C3 0.4865,2 1.0895,2 0.7517,2 C4 0.4953,2 0.9518,2 0.6806,2 C5 0.5965,2 0.8958,2 0.7388,2 C6 0.6094,2 0.7658,2 0.6650,3 C7 0.5222,2 0.6874,2 0.5292,2 C8 0.4198,2 0.7365,2 0.4721,2 C9 0.4006,2 0.8693,2 0.5474,2 C10 0.2885,2 0.92004,19 0.4943,2 C11 0.1709,2 0.83373,19 0.3681,2 C12 0.1408,2 0.8975,2 0.2741,2 C13 0.0757,2 1.0192,2 0.3300,2 C14 0.0959,2 0.71644,19 0.3455,2 C15 0.12595,19 0.66320,19 0.4462,2 C16 0.1536,2 0.7475,2 0.5841,2 C17 0.1989,2 0.6985,2 0.6762,2 C18 0.2105,2 0.5640,2 0.6372,2 C19 0.1737,2 0.4773,2 0.5000,2 C20 0.1319,2 0.52582,19 0.4049,2 C21 -0.0288,2 0.4858,2 0.1583,2 C22 -0.1365,2 0.4012,2 0.0409,2 C23 -0.2376,2 0.4521,2 -0.0182,2 C24 -0.2351,2 0.5926,2 0.0424,2 C25 -0.1252,2 0.6768,2 0.1614,2 C26 -0.0206,2 0.62716,19 0.2188,2 C27 -0.3037,3 0.7857,2 0.0136,3 C28 -0.4452,3 0.5562,3 -0.1385,3 #BOND S1 C1 1.760,2 C9 C10 1.432,3 S1 C13 1.820,2 C10 C11 1.486,3 S2 C20 1.760,2 C11 C12 1.505,3 S2 C21 1.766,2 C11 C14 1.353,3 O1 N1 1.230,3 C12 C13 1.529,3 O2 N1 1.225,3 C14 C15 1.483,3 N1 C17 1.466,3 C14 C26 1.489,3 N2 C24 1.389,3 C15 C16 1.392,3 N2 C27 1.455,4 C15 C20 1.405,3 N2 C28 1.453,4 C16 C17 1.376,3 C1 C2 1.415,3 C17 C18 1.391,3 C1 C10 1.391,3 C18 C19 1.379,3 C2 C3 1.357,3 C19 C20 1.397,3 C3 C4 1.421,3 C21 C22 1.383,3 C4 C5 1.416,3 C21 C26 1.407,3 C4 C9 1.421,3 C22 C23 1.382,3 C5 C6 1.370,4 C23 C24 1.409,3 C6 C7 1.409,4 C24 C25 1.402,3 C7 C8 1.367,3 C25 C26 1.388,3 C8 C9 1.423,3 #MDATE 951127 #CRYCON 7 26 5 5 23 30 8 9 10 11 12 13 14 15 10 7 16 17 1 17 20 21 22 23 24 21 2 27 28 29 30 20 6 6 15 16 18 19 25 26 27 32 31 32 #END d From chemistry-request@server.ccl.net Fri Jul 23 13:44:42 1999 Received: from uscmail.usc.es (uscmail.usc.es [193.144.75.8]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA12960 for ; Fri, 23 Jul 1999 13:44:38 -0400 Received: from qogolem (qogolem.usc.es [193.144.74.235]) by uscmail.usc.es (8.9.1/8.9.1) with SMTP id TAA14340 for ; Fri, 23 Jul 1999 19:40:51 +0200 (MET DST) From: "Armando Navarro" To: Subject: code for plotting Date: Fri, 23 Jul 1999 19:36:15 +0200 Message-ID: <01bed531$dd22ed00$eb4a90c1@qogolem.usc.es> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0013_01BED542.A0ABBD00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 This is a multi-part message in MIME format. ------=_NextPart_000_0013_01BED542.A0ABBD00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers: Does anyone know about fast codes for 1D plots. I am trying to represent = an array of 64K points on the screen and I have to improve the drawing = speed. Thanks in Advance ------=_NextPart_000_0013_01BED542.A0ABBD00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear = CCLers:
Does anyone know about = fast codes for=20 1D plots. I am trying to represent an array of 64K points on the screen = and I=20 have to improve the drawing speed.
 
Thanks in=20 Advance
------=_NextPart_000_0013_01BED542.A0ABBD00-- From chemistry-request@server.ccl.net Fri Jul 23 13:26:24 1999 Received: from infoviaplus.net.ar (adv18.infoviaplus.net.ar [200.9.212.60]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA12877 for ; Fri, 23 Jul 1999 13:26:19 -0400 Received: from pentiumii ([209.13.193.224]) by infoviaplus.net.ar (Tid InfoMail Exchanger v2.20) with SMTP id #932750438.093870001; Fri, 23 Jul 1999 14:20:38 -0300 Message-ID: <001a01bed52f$47f79660$e0c10dd1@pentiumii> From: "Dr. Daniel Glossman" To: Subject: molecular modeling of molecular sensor Date: Fri, 23 Jul 1999 14:17:44 -0300 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0017_01BED516.21C6B520" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 X-Infomail-Id: 932750438.24AB01AC1E039F.50438 This is a multi-part message in MIME format. ------=_NextPart_000_0017_01BED516.21C6B520 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear netter: Can somebody suggest me bibliographic references, software, WEB pages, = etc., related to the=20 computational chemistry or molecular modeling of molecular or chemical = sensors, or eventually to=20 the study of the electrical and magnetic properties of polymers? Thanks in advance = Daniel Glossman = =20 = glossman@overnet.com.ar ------=_NextPart_000_0017_01BED516.21C6B520 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear netter:
 
Can somebody suggest me bibliographic references, software, = WEB pages,=20 etc., related to the
computational chemistry or molecular modeling of molecular or = chemical=20 sensors, or eventually to
the study of the electrical and magnetic properties of = polymers?
 
Thanks in advance
 
 
           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;          Daniel=20 Glossman
            =    =20             =    =20             =    =20             =    =20             =    =20             =    =20             =    =20
           &n= bsp;           &nb= sp;           &nbs= p;            = ;            =             &= nbsp;           &n= bsp;           &nb= sp;           &nbs= p;  glossman@overnet.com.ar
=
 
 
------=_NextPart_000_0017_01BED516.21C6B520-- From chemistry-request@server.ccl.net Sun Jul 25 04:11:46 1999 Received: from chem-sci.cairo.eun.eg ([193.227.11.50]) by server.ccl.net (8.8.7/8.8.7) with SMTP id EAA28126 for ; Sun, 25 Jul 1999 04:11:38 -0400 Received: by chem-sci.cairo.eun.eg; (5.65v3.2/1.1.8.2/13Aug96-0241PM) id AA24465; Sun, 25 Jul 1999 10:10:33 +0300 Date: Sun, 25 Jul 1999 10:10:33 +0300 (EET DST) From: Adel Abbas El-Azhary Subject: Re: CCL:B3LYP/cc-pVDZ frequency scaling factors To: chemistry@CCL.NET Cc: "Qadir K. Timerghazin" In-Reply-To: Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Qadir: Please look at J. Phys. Chem., 100, 15056, 1996. Best regards, Adel El-Azhary ======================================================= > On Thu, 22 Jul 1999, Qadir K. Timerghazin wrote: > > > Dear CCLers, > > > > Does anybody know where can I find frequency scaling factor for > > B3LYP calculations with cc-pVDZ basis set? > stretches From chemistry-request@server.ccl.net Mon Jul 26 14:58:26 1999 Received: from relay2.scripps.edu (relay2.scripps.edu [137.131.200.30]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA10426 for ; Mon, 26 Jul 1999 14:58:25 -0400 Received: from elvis.scripps.edu (elvis.scripps.edu [137.131.130.25]) by relay2.scripps.edu (8.9.3/TSRI-3.0.2r) with ESMTP id LAA26887 for ; Mon, 26 Jul 1999 11:54:01 -0700 (PDT) Received: from scripps.edu (localhost [127.0.0.1]) by elvis.scripps.edu (8.9.2/TSRI-3.0) with ESMTP id LAA72307 for ; Mon, 26 Jul 1999 11:54:03 -0700 (PDT) Sender: yadavm@scripps.edu Message-ID: <379CAECA.EEE93F05@scripps.edu> Date: Mon, 26 Jul 1999 11:54:03 -0700 From: Maneesh Yadav X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: chemistry@ccl.net Subject: What is a good system to get for computational chemistry? Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit (If there is already a good summary for this please let me know, otherwise please send answers directly to me and let me post a summary to save space and flamewars:) Hello all, I will be returning to Toronto in September but I will continue working for my boss remotely and he will also be buying me a machine for computational chemistry type work. My question is what type of system should I get (we have about 3k to spend)? I use an octane right now, and I am finding that there is a lot of (even non-graphical) computational chemistry software out there for specifically for SGI...but (this was a qualitative test) I find that the SGI's perhaps are not so fast in terms of raw computing power (the R10K in my octane seems to be only slightly faster than the PII in one of our PC's (just from what I can tell in rendering an animation in POV))? I am considering an Alpha+openGL+linux, does anyone have experience with such a system (right now I am doing mostly docking type stuff and modelling of small (10's of residues) peptide systems) and the amount of available software for chemistry? Or I could take a PC+linux based approach (definately cheaper, but Mesa hardware suppourt is limited)? What about a dual Xeon? The other nice thing is that we have a insightII license at scripps that would be nice to be able to take advantage of when I need it; but I guess I can only do that if I go with an SGI. My real concern is the performance of graphics applications on non SGI's... So basically if somone has had or is having experience with any of these systems with computational chemistry (mainly docking simulation and modelling) if you let me know a good way to spend 3k that'd be awful nice.. -Many thanks Maneesh From chemistry-request@server.ccl.net Mon Jul 26 15:33:18 1999 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA10864 for ; Mon, 26 Jul 1999 15:33:16 -0400 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (980427.SGI.8.8.8/980728.SGI.AUTOCF) via ESMTP id VAA03236 for ; Mon, 26 Jul 1999 21:45:37 +0200 (CEST) Date: Mon, 26 Jul 1999 21:45:37 +0200 From: Christian Pilger To: chemistry@ccl.net Subject: msi file format In-Reply-To: <199907232136.SAA03776@ibitipoca.fisica.ufjf.br> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers, I would like to convert SYBYL-mol2 files either into Insight-CAR format or preferably directly into Cerius2-MSI format. Here is what I've tried so far: * BABEL: neither CAR- nor MSI-Format is supported for output * CACTVS: does not recognize the mol2-files generated by SYBYL (!) * mol2mol: the CAR-output of this program does not contain the correct connectivities Any ideas ? Did anybody face similar problems ? Can somebody provide me with a hint where I can find a detailed description of the Cerius2-MSI file format ? Any suggestions are appreciated ! Best wishes, Christian ----------------------------------------------------------------- Dipl.-Chem. Christian Pilger Uni-GH Paderborn FB 13 - Organische Chemie Warburger Str. 100 D-33098 Paderborn/Germany Tel.: 05251-60279/-602183 Fax : 05251-603245 email: cpilger@oc30.uni-paderborn.de Word Wide Web: http://oc30.uni-paderborn.de/~cpilger ----------------------------------------------------------------- From chemistry-request@server.ccl.net Mon Jul 26 01:57:43 1999 Received: from deews1.dent.okayama-u.ac.jp (deews1.dent.okayama-u.ac.jp [150.46.202.36]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA03697 for ; Mon, 26 Jul 1999 01:57:38 -0400 Received: from [150.46.162.72] ([150.46.162.72]) by deews1.dent.okayama-u.ac.jp (8.9.2/3.7Wpl2-oucc-1.0) with SMTP id OAA22597 for ; Mon, 26 Jul 1999 14:53:09 +0900 (JST) Date: Mon, 26 Jul 1999 14:53:09 +0900 (JST) Message-Id: <199907260553.OAA22597@deews1.dent.okayama-u.ac.jp> To: CHEMISTRY@server.ccl.net From: ep7@dent.okayama-u.ac.jp (Masamura) X-Sender: ep7@dent.okayama-u.ac.jp (Unverified) Subject: Re: Summary of Ion-water clusters MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Sir: One useful answer for my question (Please teach me the recent literatures and reviews of ion-water clusters) was gotted. ******************************************************* Date: Mon, 19 Jul 1999 11:27:08 -0600 (MDT) From: Cory Pye X-Sender: cory@acs5.acs.ucalgary.ca To: Masamura Subject: Re: CCL:Ion-water clusters Content-Type: TEXT/PLAIN; charset=US-ASCII X-UIDL: =$#!!\$Sd9From my own work: CC Pye, IJQC, 1999, in press : Li-X hydration CC Pye et al, JPC A 1998, 102, 9933-9943: Mg hydration WW Rudolph et al, JPC B 1998, 102, 3564-3573: Cd hydration CC Pye et al, JPC 1996, 100, 601-605: Li hydration W Rudolph et al, JPC 1995, 99, 3793-3797: Li Raman + some ab initio ************* ***************** ! Dr. Cory C. Pye *** ** ** ** ! Postdoctoral Fellow ** * **** ! Theoretical and Computational Chemistry ** * * ! cory@ucalgary.ca ** * * ! http://www.cobalt.chem.ucalgary.ca/cory *** * * ** ! ***************** ! Les Hartree-Focks ************* ! (Apologies to Montreal Canadien Fans) ******************************************************** *********************************** M. Masamura Department of Preventive Dentistry Okayama University Dental School Shikata-cho 2-5-1, Okayama, 700-8525 Japan *********************************** From chemistry-request@server.ccl.net Mon Jul 26 07:42:48 1999 Received: from mel.ruc.dk (mel.ruc.dk [130.225.220.27]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA06586 for ; Mon, 26 Jul 1999 07:42:48 -0400 Received: from virgil.ruc.dk (virgil.ruc.dk [130.225.220.110]) by mel.ruc.dk (8.9.3/8.9.1) with ESMTP id NAA21725; Mon, 26 Jul 1999 13:38:29 +0200 (MET DST) Received: from VIRGIL/SpoolDir by virgil.ruc.dk (Mercury 1.40); 26 Jul 99 13:39:21 +0100 Received: from SpoolDir by VIRGIL (Mercury 1.40); 26 Jul 99 13:39:16 +0100 From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: chemistry@ccl.net, "E. Lewars" Date: Mon, 26 Jul 1999 13:38:48 +0100 Subject: CCL:CALC RAMAN ACTIVITIES__HOW GOOD? Priority: normal X-mailer: Pegasus Mail for Windows (v2.23) Message-ID: Dear CCL: E. Lewars asked the following question (1999 July 25): > INTENSITIES OF IR BANDS--HOW GOOD? > > A lot has been published on correction factors for the *positions* (i.e. the > wavenumber values) of calculated IR bands; the canonical paper is A. P. Scott > and L. Radom, J. Phys. Chem., 1996, 100, 16502. > Has there been any published work on the the *relative intensities* of > calculated IR bands? I mean purely empirical comparison of calc and experimental > IR spectra, to see which methods give the best match to the real spectra, and > how, if possible, one can correct calc intensities to match the experimental. I would like to add the corresponding question concerning *Raman scattering activities*! Thank you, Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Phone: +45 4674 2000 (RUC) Department of Chemistry +45 4674 2710 (direct) Roskilde University (RUC) Fax: +45 4674 3011 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://www.rub.ruc.dk/dis/chem/psos/ =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From chemistry-request@server.ccl.net Mon Jul 26 12:36:36 1999 Received: from bioem.ing.uniroma1.it (bioem.ing.uniroma1.it [151.100.8.36]) by server.ccl.net (8.8.7/8.8.7) with SMTP id MAA08477 for ; Mon, 26 Jul 1999 12:36:34 -0400 Received: from daniele (a-rm23-29.tin.it [212.216.166.156]) by bioem.ing.uniroma1.it (950413.SGI.8.6.12/950213.SGI.AUTOCF) via SMTP id SAA28691 for ; Mon, 26 Jul 1999 18:43:49 -0700 Message-ID: <006001bed783$38b18c00$0d01a8c0@elettra.it> From: "Daniele Spera" To: "CCL" Subject: dielectric permittivity through MD Date: Mon, 26 Jul 1999 18:23:38 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_005D_01BED793.FB2DCE00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2014.211 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2014.211 This is a multi-part message in MIME format. ------=_NextPart_000_005D_01BED793.FB2DCE00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi dear CCLers, hope someone can point me to some interesting reviews and papers about = dielectric permittivity measuraments technics through Molecular Dynamics = simulations. Thank you. I will summarize any response. Daniele Spera _____________________________________ Dott. Ing. Daniele Spera Rome University "La Sapienza" E-mail: daniele@bioem.ing.uniroma1.it ------=_NextPart_000_005D_01BED793.FB2DCE00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi dear CCLers,
 
hope someone can point me to some = interesting=20 reviews and papers about dielectric permittivity measuraments technics = through=20 Molecular Dynamics simulations. Thank you. I will summarize any=20 response.
 
Daniele Spera
 
_____________________________________
Dott.=20 Ing. Daniele Spera
Rome University "La Sapienza"
E-mail: daniele@bioem.ing.uniroma1.= it
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