From chemistry-request@server.ccl.net Tue Jul 27 04:20:17 1999 Received: from mail.rwth-aachen.de (mail.RWTH-Aachen.DE [137.226.144.9]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id EAA16635 for ; Tue, 27 Jul 1999 04:20:15 -0400 Received: from ac.rwth-aachen.de (kazhad-dum.ac.RWTH-Aachen.DE) by mail.rwth-aachen.de (PMDF V5.1-12 #D3869) with ESMTP id <01JE209U5DRY00006D@mail.rwth-aachen.de> for CHEMISTRY@ccl.net; Tue, 27 Jul 1999 10:13:17 +0200 Date: Tue, 27 Jul 1999 10:16:43 +0200 From: Tatus Subject: b3lyp convergence in g9? Sender: krzys@mail.rwth-aachen.de To: CCL Message-id: <379D6AEB.F549EA4A@ac.rwth-aachen.de> Organization: Inst. Inorg. Chem., RWTH Aachen, Germany MIME-version: 1.0 X-Mailer: Mozilla 4.51 [en] (X11; I; Linux 2.2.5-15 i686) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Dear Collegues, I did some calculations useing b3lyp method. Quite frequently I got problem with max & RMS displacement criteria. They are frozen on some value and additional iterations couldn't change it. Opt=CalcAll or generating new input-file wasn't helpfull. The same calculation (molecule) converged without any problem on HF-level. Without success was also trial with opt=tight scf=tight. Any other idea how to make my calculation to converge? Interesting are two lines from log-file: Cartesian Forces: Max 0.000142350 RMS 0.000027962 Internal Forces: Max 0.000001544 RMS 0.000000431 My calculations are done in Z-Matrix. Why are there so big differeces bettween values for cartesian and internal coordiantes? Thanks in advance, Krzysztof Radacki From chemistry-request@server.ccl.net Tue Jul 27 11:18:46 1999 Received: from wugate.wustl.edu (wugate.wustl.edu [128.252.120.1]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA19993 for ; Tue, 27 Jul 1999 11:18:46 -0400 Received: from mirlink.wustl.edu (mirlink.wustl.edu [128.252.155.1]) by wugate.wustl.edu (8.8.8/8.8.5) with SMTP id KAA00488 for ; Tue, 27 Jul 1999 10:14:13 -0500 (CDT) Message-ID: Date: 27 Jul 1999 10:13:40 -0500 From: "David Reichert" Subject: Dock4.0.1 & sdf2mol2 To: "CCL post" X-Mailer: Mail*Link SMTP-MS 3.0.2 Mime-Version: 1.0 Content-Type: text/plain; charset="ISO-8859-1"; Name="Message Body" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id LAA19994 Hi, Hopefully someone on the list can provide some insight. I've recently installed Dock version 4.0.1 on my SGI and a linux box everything compiled allright and seems to work normally. Here's the problem I'm unable to get the prgram sdf2mol2 to run, it compiles OK but when I try to convert some sd files from NCI (nciopen3d, stdmech3d) the program starts up and then crashes with a core dump. Babel can convert these files so I think the problem is with sdf2mol2. Anyone have any pointers or tips ? thanks in advance, Dave Reichert ____________________________________________ | David Reichert, Ph.D | | Mallinckrodt Institute of Radiology | | Washington University School of Medicine | | St. Louis, MO | | | | e-mail: reichertd@mirlink.wustl.edu | | voice: (314) 362-8461 | | fax: (314) 362-9940 | ____________________________________________ From chemistry-request@server.ccl.net Mon Jul 26 17:29:50 1999 Received: from theory.tc.cornell.edu (THEORY.TC.CORNELL.EDU [128.84.30.174]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA12949 for ; Mon, 26 Jul 1999 17:29:50 -0400 Received: from oncidium (ONCIDIUM.TC.CORNELL.EDU [128.84.181.31]) by theory.tc.cornell.edu (8.8.4/8.8.3/CTC-1.0) with SMTP id QAA15033; Mon, 26 Jul 1999 16:07:07 -0400 Message-Id: <3.0.3.32.19990726160607.0092e100@tc.cornell.edu> X-Sender: cal@tc.cornell.edu X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Mon, 26 Jul 1999 16:06:07 -0400 To: cal@tc.cornell.edu From: Linda Callahan Subject: Workshop Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" The Parallel Processing Resource for Biomedical Scientists at the Cornell Theory Center (CTC) will hold a workshop on Nov 15-16 at Cornell that will provide an in-depth description and hands-on experience with the software packages that the resource just released to the public domain (see http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/). Since the capacity of the modeling class is limited, we may be unable to accept all applications. Therefore, please register early at http://www.tc.cornell.edu/Events/1999/CompBiologyTools/. The registration is free for academic users and is $750 for participants >from for-profit organizations; $500 for members of CTC's Corporate Program. Each lecture will be followed by hands-on experiment of the participans in an lab equipped with SGI workstations. Tentative list of lectures: Jaroslaw Meller. Sequence and structure alignment and linear optimization of potentials and score function. Optimization of gap energies. Overview of LOOPP - a program for Linear Optimization Of Protein Potentials Jooyoung Lee. Conformational sampling, reduced and detailed representation of proteins, CASP3 results, the program CSA - Conformational Space Annealing. Daniel Ripoll and Czarek Czaplewski. Analysis of torsional space and energy calculations of protein conformations. Application of ECEPPAK and ANALYZE. Global conformational searches using MCM and EDMC Jarek Pillardy. Deformation-based global optimziation (SCBDBM) and applications to crystals and peptides. Examples will include global optimization of crystals of small molecules and for polyalanine with the program UNRE. Ron Elber. Introduction to the structure of MOIL. Possible applications, limitations and advantages. Future directions of the code. Veaceslav Zaloj. The NT environment of MOIL. Veaceslav Zaloj. Computations of long-time dynamics of biological molecules by stochastic path optimization. The parallel use of the STO program in MOIL. Jaroslaw Meller. The use of Locally Enhanced Sampling to explore diffusion pathways in the protein myoglobin. From chemistry-request@server.ccl.net Mon Jul 26 23:45:02 1999 Received: from ozone.umsl.edu (ozone.umsl.edu [134.124.105.185]) by server.ccl.net (8.8.7/8.8.7) with SMTP id XAA15020 for ; Mon, 26 Jul 1999 23:45:02 -0400 Received: from ozone.umsl.edu (indy1.umsl.edu [134.124.105.162]) by ozone.umsl.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) via ESMTP id MAA08755; Mon, 28 Jun 1999 12:17:24 -0700 Sender: wang@ozone.umsl.edu Message-ID: <379D4606.A855FCC1@ozone.umsl.edu> Date: Mon, 26 Jul 1999 22:39:20 -0700 From: Wang Xia Organization: UMSL X-Mailer: Mozilla 4.07 [en] (X11; U; IRIX 6.2 IP22) MIME-Version: 1.0 To: Christian Pilger CC: chemistry@ccl.net Subject: Re: CCL:msi file format References: Content-Type: multipart/alternative; boundary="------------2B921D6357D87C1E34D8D7C5" --------------2B921D6357D87C1E34D8D7C5 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit You may try next process: 1. Save any mol2 file (for example, a file named test.mol2) as MACCS file format in SYBYL, using save as command. Then you will get a file name test.mac. 2. Rename this file test.mac to test.sd. Then read this test.sd file in Cerius2 (using Load Model, chose MACCS as file format, where *.sd and *.mol as default format) 3. Save this file as MSI format just in Cerius2, you would get a file named test.msi. If you have many mol2 format molecule, and want them all to be converted into MSI format, you can put them in a Spreadsheet, then save them as SD file in SYBYL, which can be read through Cerius2, then to MSI format. Thanks. Sincerely, Xia Wang Christian Pilger wrote: > 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 > > ----------------------------------------------------------------- > > -= 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 -- ________________________________________________________________________ Wang Xia * 8209-F, Normandy Trace Ct. Department of Chemistry, * St. Louis University of Missouri-St. Louis, * Missouri, 63121 8001 Natural Bridge Road, * USA St. Louis * Tel: (314) 5166882 (Lab.) Missouri, 63121 * (314) 5241178 (Hom.) USA * Fax: (314) 5165342 ________________________________________________________________________ --------------2B921D6357D87C1E34D8D7C5 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit You may try next process:
1. Save any mol2 file (for example, a file named test.mol2) as MACCS file format in SYBYL, using save as command. Then you will get a file name test.mac.
2. Rename this file test.mac to test.sd. Then read this test.sd file in Cerius2 (using Load Model, chose MACCS as file format, where *.sd and *.mol as default format)
3. Save this file as MSI format just in Cerius2, you would get a file named test.msi.
If you have many mol2 format molecule, and want them all to be converted into MSI format, you can put them in a Spreadsheet, then save them as SD file in SYBYL, which can be read through Cerius2, then to MSI format.
Thanks.

Sincerely,
Xia Wang

Christian Pilger wrote:

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

-----------------------------------------------------------------

-= 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

-- 
________________________________________________________________________
                                  
 Wang Xia                           *    8209-F, Normandy Trace Ct. 
 Department of Chemistry,           *    St. Louis 
 University of Missouri-St. Louis,  *    Missouri, 63121  
 8001 Natural Bridge Road,          *    USA 
 St. Louis                          *    Tel: (314) 5166882 (Lab.) 
 Missouri, 63121                    *         (314) 5241178 (Hom.) 
 USA                                *    Fax: (314) 5165342  
________________________________________________________________________
  --------------2B921D6357D87C1E34D8D7C5-- From chemistry-request@server.ccl.net Mon Jul 26 18:26:26 1999 Received: from web125.yahoomail.com (web125.yahoomail.com [205.180.60.193]) by server.ccl.net (8.8.7/8.8.7) with SMTP id SAA13313 for ; Mon, 26 Jul 1999 18:26:26 -0400 Message-ID: <19990726222346.13891.rocketmail@web125.yahoomail.com> Received: from [208.165.103.2] by web125.yahoomail.com; Mon, 26 Jul 1999 18:23:46 EDT Date: Mon, 26 Jul 1999 18:23:46 -0400 (EDT) From: Gustavo Mercier Reply-To: gamercier@yahoo.com Subject: Fwd: Re: Fwd: Amber 5.0 Makefile PGC compiler? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi! Several people asked me for the Machine file to compile AMBER 5.0 under the PGC compiler. DEK at ucsf replied with the file listed below. Obviously you must get rid of the header and ">" at the begining of the lines. Good LucK Gus Mercier, Jr. --- dek@cgl.ucsf.edu wrote: > To: gamercier@yahoo.com > Reply-to: dek@cgl.ucsf.edu > From: dek@cgl.ucsf.edu > Subject: Re: Fwd: Amber 5.0 Makefile PGC compiler? > Date: Wed, 14 Jul 1999 14:52:51 -0700 > > > here is my MACHINE.pgcc > > > #! /bin/csh -f > ######################################################################## > # > # > # Copyright (c) 1986, 1991, 1995 > # > # Regents of the University of California > # > # > # > # All Rights Reserved > # > # > # > # Machine Dependency Handling System > # > # > # > # Bill Ross ross@cgl.ucsf.edu > # > # An extension of work of George Seibel > # > # > # > # Dependencies written by various authors. > # > # > # > # Permission to use, copy, modify, and distribute > this software and # > # its documentation for any purpose and without fee > is hereby # > # granted, provided that the above copyright notice > appear in all # > # copies and that both that copyright notice and > this permission # > # notice appear in supporting documentation, and > that the name of # > # the University of California not be used in > advertising or # > # publicity pertaining to distribution of the > software without # > # specific, written prior permission. > # > # > # > # THE REGENTS OF THE UNIVERSITY OF CALIFORNIA > DISCLAIM ALL # > # WARRANTIES WITH REGARD TO THIS SOFTWARE, > INCLUDING ALL IMPLIED # > # WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO > EVENT SHALL THE # > # UNIVERSITY OF CALIFORNIA BE LIABLE FOR ANY > SPECIAL, INDIRECT OR # > # CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER > RESULTING FROM # > # LOSS OF USE, DATA OR PROFITS, WHETHER IN AN > ACTION OF CONTRACT, # > # NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT > OF OR IN # > # CONNECTION WITH THE USE OR PERFORMANCE OF THIS > SOFTWARE. # > # > # > ######################################################################## > > setenv MACHINE "Linux MPI" > setenv MACH F2C > setenv MACHINEFLAGS " -DISTAR2 -DREGNML -DEWALD > -DHAS_FTN_ERFC" > > > > # CPP is the cpp for this machine > setenv CPP "/lib/cpp -traditional" > > > # SYSDIR is the name of the system-specific source > directory relative to src/*/ > setenv SYSDIR Machine/f2c > > # COMPILER ALIASES: > setenv FC "pgf77" > setenv CC "pgcc" > > # LOADER/LINKER: > setenv OPT "-O3 -Munroll -Mnoframe -tp p6 -pc 64" > setenv LOAD "$FC $OPT" > setenv LOADLIB "-lm" > > # little or no optimization: > setenv L0 "$FC -c " > setenv L1 "$FC -c $OPT" > setenv L2 "$FC -c $OPT" > setenv L3 "$FC -c $OPT" > > # ranlib, if it exists > setenv RANLIB ranlib > > # spasms configuration > #SPASMS MACHINE.f2c_spasms_config > #SPASMS unix > #SPASMS n390 > #SPASMS large > === -- ("`-/")_.-'"``-._ Gustavo A. Mercier,Jr.,MD,PhD (. . `) -._ )-;-,_() Hillcrest Medical Center (v_,)' _ )`-.\ ``- Dept. of Radiology _;- _,-_/ / ((,' Tulsa X-Ray Laboratory ((,.-' ((,/ 5840 South Memorial Suite 301 gamercier@yahoo.com Tulsa, OK 74145-9082 voice: 918-664-9892/fax: 918-664-6120 _________________________________________________________ Do You Yahoo!? Get your free @yahoo.com address at http://mail.yahoo.com From chemistry-request@server.ccl.net Tue Jul 27 02:34:05 1999 Received: from popcsi.unian.it (root@popcsi.unian.it [193.205.128.17]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id CAA15929 for ; Tue, 27 Jul 1999 02:34:04 -0400 Received: from anvax1.unian.it ([193.205.128.181]) by popcsi.unian.it (8.8.7/8.8.7) with SMTP id IAA02717 for ; Tue, 27 Jul 1999 08:21:24 +0200 Message-Id: <3.0.32.19990727083501.007a7630@popcsi.unian.it> X-Sender: roberta@popcsi.unian.it X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Tue, 27 Jul 1999 08:35:01 +0200 To: chemistry@ccl.net From: Roberta Galeazzi Subject: SUMMARY: AM1 and LUMOs Mime-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id CAA15930 Dear CCLers, here is the summary of the only answer I've got about my question. Howewer I found this article very interesting and useful and I would like to thank Karl for his kind reply. Hope this help Cheers, Roberta **************************ORIGINAL QUESTION********************************** Dear CCLs, could anyone give some references about the reliability of the AM1 method in calculating both shape and energy of LUMOs? *************** ANSWERS ******************************************** Dr. Galeazzi, I have one article here that addresses the energetics of both HOMO and LUMO: Clare, B.W. Theor Chim Acta 87 (1994) 415-430. Hope this helps. Cheers, Karl ************************************************************************** **************************************************************************** ******* Dr. Roberta Galeazzi Università di Ancona Dipartimento di Scienze dei Materiali e della Terra via Brecce Bianche I-60131 Ancona ITALY tel.: +39-71-2204707 fax: +39-71-2204714 e-mail: roberta@popcsi.unian.it From chemistry-request@server.ccl.net Tue Jul 27 07:03:28 1999 Received: from mail2.organik.uni-erlangen.de (lesath.organik.uni-erlangen.de [131.188.128.212]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA18396 for ; Tue, 27 Jul 1999 07:03:21 -0400 Received: from wtewael.organik.uni-erlangen.de (wtewael [131.188.128.216]) by mail2.organik.uni-erlangen.de (8.8.8/8.1.4-FAU) with ESMTP id MAA11860 for ; Tue, 27 Jul 1999 12:58:32 +0200 (MET DST) Received: (from wdi@localhost) by wtewael.organik.uni-erlangen.de (8.8.7/8.1.59-FAU) id KAA11225 for chemistry@ccl.net; Tue, 27 Jul 1999 10:58:31 GMT From: "Wolf-Dietrich Ihlenfeldt" Message-Id: <9907271258.ZM11223@torvs.ccc.uni-erlangen.de> Date: Tue, 27 Jul 1999 12:58:31 -0600 In-Reply-To: Christian Pilger "CCL:msi file format" (Jul 26, 21:45) References: Reply-To: Wolf-Dietrich.Ihlenfeldt@CCC.Chemie.Uni-Erlangen.DE X-Phones: +49-9131-85-6579 X-Fax: +49-9131-85-6566 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: chemistry@ccl.net Subject: Re: CCL:msi file format Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 8bit On Jul 26, 21:45, Christian Pilger wrote: > Subject: CCL:msi file format > 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 (!) This is not true. CACTVS does support sybyl2 molfiles, but this is a format which is not loaded by default (I/O is implemented as modules). Either use the 'I/O Module Manager' in the File menu of newer CACTVS tools releases to load the sybyl2 modile temporarily (or permanently for all future tool invocations) or to unload other unneeded modules, or add a line 'filex load sybyl2' to your converter scripts, or edit the file 'cactvsio' in the siteconfig directory in the unpacked distribution. > * 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 > > ----------------------------------------------------------------- > > -= 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 > >-- End of excerpt from Christian Pilger -- Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-26579 Fax (+49)-(0)9131-85-26566 --- The three proven methods for ultimate success and fame: 1) Nakanu nara koroshite shimae hototogisu 2) Nakanu nara nakasete miseyou hototogisu 3) Nakanu nara naku made matou hototogisu From chemistry-request@server.ccl.net Tue Jul 27 10:42:06 1999 Received: from zeus.fcq.unc.edu.ar (zeus.fcq.unc.edu.ar [200.16.18.54]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA19709 for ; Tue, 27 Jul 1999 10:42:02 -0400 Received: from localhost by zeus.fcq.unc.edu.ar; (5.65/1.1.8.2/27Feb98-1006AM) id AA00750; Tue, 27 Jul 1999 11:36:50 -0500 Sender: mariano@zeus.fcq.unc.edu.ar Message-Id: <379DE01E.41C6@zeus.fcq.unc.edu.ar> Date: Tue, 27 Jul 1999 11:36:47 -0500 From: "Domingo Mariano A. Vera" X-Mailer: Mozilla 3.01Gold (X11; I; OSF1 V3.0 alpha) Mime-Version: 1.0 To: chemistry@ccl.net Subject: virtual orbitals and DFT Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi Folks I have a little question that I previously asked in a post grade course and in a bar but I never got a definitive answer. How much reliable are (or how much sense they have) the virtual orbitals from a DFT calculation? More specifically, consider non local, state of the art, mixed formalisms (using the hf density) such as blyp, b3lyp or PDB (with standar all electron basis), for example. I noted that for critical systems (open shell, net charge, high correlation effects) such as some radical anions, at least the LUMO up to LUMO+2 have the same energy pattern and the coefficients are very similar to MP2. Best regards Mariano. -- D. Mariano A. Vera INFIQC / Departamento de Quimica Organica Facultad de Ciencias Quimicas - Universidad Nacional de Cordoba. Ciudad Universitaria - 5000 Cordoba - ARGENTINA. Voice: 54-351-4334170 Fax: 54-351-4333030 mariano@zeus.fcq.unc.edu.ar From chemistry-request@server.ccl.net Tue Jul 27 14:34:37 1999 Received: from mail.chemie.fu-berlin.de (root@mail.chemie.fu-berlin.de [160.45.24.23]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA21922 for ; Tue, 27 Jul 1999 14:34:36 -0400 Received: from ki1.chemie.fu-berlin.de ([160.45.24.21]) (1438 bytes) by mail.chemie.fu-berlin.de via sendmail with P:smtp/R:bind_hosts/T:inet_zone_bind_smtp (sender: ) id for ; Tue, 27 Jul 1999 20:29:58 +0200 (CEST) (Smail-3.2.0.101) Received: by ki1.chemie.fu-berlin.de (Smail3.2.0.98) from chemie.fu-berlin.de (160.45.24.178) with esmtp id ; Tue, 27 Jul 1999 20:29:57 +0200 (MEST) Sender: rabe@ccl.net Message-ID: <379DFAA4.896F8704@chemie.fu-berlin.de> Date: Tue, 27 Jul 1999 20:29:56 +0200 From: Bjoern Rabenstein Organization: Freie Universitaet Berlin, Germany X-Mailer: Mozilla 4.51 [en] (X11; U; Linux 2.2.9 i686) X-Accept-Language: de MIME-Version: 1.0 To: Computational Chemistry Mailing List Subject: Distances along a solvent accessible surface Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear CCLers! I need to calculate the shortest possible distance that a particle must travel along a solvent accessible surface to get from one point of the surface to another. Does anybody know methods (or even programs) to do that? Or can anybody give me a hint where I can find suitable literature? Thanks for any help! -- __ \__\__ \ Bjoern Rabenstein * PhD student * Freie Universitaet Berlin __\___\__\_\ Inst. f. Kristallographie * Takustrasse 6 * D-14195 Berlin \ \ \ \\ [email] rabe@chemie.fu-berlin.de [phone] +49-30-838-3484 [WWW] http://userpage.chemie.fu-berlin.de/~rabe/ [fax] +49-30-838-3464