From laiter@isis.rti.org Mon Sep 25 12:19:32 1995 Received: from rtifs2.rti.org for laiter@isis.rti.org by www.ccl.net (8.6.10/950822.1) id MAA22519; Mon, 25 Sep 1995 12:19:29 -0400 Received: by rtifs2.rti.org (5.65/DEC-Ultrix/4.3) id AA29651; Mon, 25 Sep 1995 12:14:16 -0400 Received: by cdse14.rti.org (5.65/DEC-Ultrix/4.3) id AA13738; Mon, 25 Sep 1995 12:22:45 -0400 Received: by isis.rti.org (931110.SGI/930416.SGI.AUTO) for @rtifs2.rti.org:chemistry@www.ccl.net id AA02024; Mon, 25 Sep 95 12:13:16 -0400 Date: Mon, 25 Sep 95 12:13:16 -0400 From: laiter@isis.rti.org (Sergei Laiter[Lighter]) Message-Id: <9509251613.AA02024@isis.rti.org> Subject: G92 B3LYP calculations for iodine with ECP To: chemistry@www.ccl.net Dear Netters, I'm performing G92 B3LYP calculations for iodine with ECP and get the following messages: "No unpruned grid is available for this atom. No unpruned grid is available for this atom. No unpruned grid is available for this atom. No unpruned grid is available for this atom. No unpruned grid is available for this atom. No unpruned grid is available for this atom. No unpruned grid is available for this atom." I do get the job completed, but I'd really appriciate it if someone would explain to me what this message means and what the consequences are. -Sergei From owner-chemistry@ccl.net Tue Sep 26 03:49:51 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id DAA04824; Tue, 26 Sep 1995 03:49:46 -0400 Received: from csb0.IPC.PKU.EDU.CN for ldw@csb0.IPC.PKU.EDU.CN by bedrock.ccl.net (8.6.10/950822.1) id DAA24588; Tue, 26 Sep 1995 03:49:40 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@ccl.net id AA27841; Tue, 26 Sep 95 15:29:00 -0700 Date: Tue, 26 Sep 1995 15:28:59 -0700 (PDT) From: ldw To: chemistry@ccl.net Subject: Small peptide dynamics Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Sun, 24 Sep 1995, Charles Martin wrote: >>> Dawei Lin writes.. >>> >>> I want to do molecular dynamics calculation of small peptides(lenght 5 >>> to 8). Before I set out to do the calculations, I like to listen any of >>> your suggests or experences. >>> ....... >> >> I would be most interested in reading other opinions and >>seeing other pieces of evidence, pro and/or contrary. Anyone? >> >> Chuck Martin >> > > As I understood the original question, the problem is in performing > the comprehensive conformational search for peptides of small size. In my > experience, the problem is mainly not in the force field parameters, but > in calculation protocols. > > >Gregory V. Nikiforovich Phone (314) 935-4677 >Research Professor Fax (314) 935-4979 >Center for Molecular Design E-mail address: >Washington University gregory@wucmd.wustl.edu >Lopata Hall, Box 1099 >St.Louis, MO 63130 In fact, I want to use MD to compare small peptides' flexibilty. The original idea is that I use SAME conditions to do MD calculation to serval same length small peptides, such as same heatting time, same equlibrition time and same sampling method etc. After that I do clustering calculation to all the conformations of each peptide, and then analysis the cluster result. Maybe the peptides which conformations have less clusters will be more fix ones, and peptides which conformations have more clusters will be flexible ones. Is that idea resonable? Dawei ---------- *** Dawei LIN *** ------------------ Ph.D student of Molecular Design Lab Institute of Physical chemistry Peking University Beijing 100871 P.R.China Phone: 86-10-2501490 Fax: 86-10-2501725 Email: ldw@ipc.pku.edu.cn ldw@pschnetware.pku.edu.cn URL: http://www.ipc.pku.edu.cn/ldw/ldw.htm ------------------------------------------------ From owner-chemistry@ccl.net Tue Sep 26 04:21:22 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA04951; Tue, 26 Sep 1995 04:16:57 -0400 Received: from comsun.rz.uni-regensburg.de for herbert.homeier@rchs1.chemie.uni-regensburg.de by bedrock.ccl.net (8.6.10/950822.1) id EAA24650; Tue, 26 Sep 1995 04:16:42 -0400 Received: from rchs1.chemie.uni-regensburg.de by comsun.rz.uni-regensburg.de with SMTP id AA20085 (5.65c/IDA-1.4.4 for ); Tue, 26 Sep 1995 09:16:05 +0100 Received: by rchs1.chemie.uni-regensburg.de (4.1/URRZ-sub (1.5)) id AA25710; Tue, 26 Sep 95 09:13:27 +0100 Date: Tue, 26 Sep 95 09:13:27 +0100 From: Herbert Homeier t4720 Message-Id: <9509260813.AA25710@rchs1.chemie.uni-regensburg.de> To: jmolina@ciusa.edu.ar Subject: Re: xray Cc: CHEMISTRY@ccl.net > CCL:X-Rays > > jmolina@ciunsa.edu.ar > Fri, 22 Sep 1995 20:46:19 -0300 > > Hi, > I would like to recieve any references about computer programmes dealing with > X RAys data interpretation for structure determination. > Thanks for your attention. > Jose Molina > e-mail: jmolina\@ciunsa.edu.ar > > ===================================================== > Universidad Nacional de Salta > Calle Buenos Aires 177 > 4400 Salta - ARGENTINA > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: jkl@ccl.net > -- Original Sender From: Address: jmolina@ciunsa.edu.ar > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: > Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: > www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > Dear Dr. Molina, may I draw your attention to the fact that there is a WWW server devoted to Xray questions. It may well be that you find an answer to your question there. Another good starting point may be the Computer Physics Communications Program Library. Links to these places may be found in the list of Chemistry Servers and Resources, URL: http://rchs1.uni-regensburg.de/external.html (use your browser to search for "X-Ray", "CPC"). Best regards Herbert Homeier -------------------------------------------------------------- Dr. Herbert H. H. Homeier Institut fuer Physikalische und Theoretische Chemie Universitaet Regensburg D-93040 Regensburg, Germany Phone: +49-941-943 4720 FAX : +49-941-943 2305 email: na.hhomeier@na-net.ornl.gov HOMEPAGE --------------------------------------------------------------- From owner-chemistry@ccl.net Tue Sep 26 04:34:52 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id EAA05120; Tue, 26 Sep 1995 04:34:01 -0400 Received: from shiva.jussieu.fr for fanny@ccr.jussieu.fr by bedrock.ccl.net (8.6.10/950822.1) id EAA24688; Tue, 26 Sep 1995 04:33:57 -0400 From: Received: from moka.ccr.jussieu.fr (moka.ccr.jussieu.fr [134.157.1.23]) by shiva.jussieu.fr (8.6.10/jtpda-5.1) with ESMTP id JAA07884 for ; Tue, 26 Sep 1995 09:33:38 +0100 Received: from [134.157.50.121] (boris.urbb.jussieu.fr [134.157.50.121]) by moka.ccr.jussieu.fr (8.6.11/jtpda-5.1) with SMTP id JAA32189 for ; Tue, 26 Sep 1995 09:33:35 +0100 Message-Id: <199509260833.JAA32189@moka.ccr.jussieu.fr> Date: Tue, 26 Sep 1995 09:35:19 +0100 To: chemistry@ccl.net Subject: pdb format Dear Netters, .............. ............... ............. ATOM 32 H32 MOL 1 -0.612 -0.857 1.836 ATOM 33 H33 MOL 1 4.013 -0.975 2.204 ATOM 34 H34 MOL 1 1.846 0.099 -1.086 ATOM 35 H35 MOL 1 2.172 2.546 2.999 ATOM 36 H36 MOL 1 3.299 1.175 3.421 ATOM 37 H37 MOL 1 5.114 0.890 1.211 ATOM 38 H38 MOL 1 7.103 2.190 0.462 ATOM 39 Cl39MOL 1 7.694 4.963 0.723 ATOM 40 H40 MOL 1 5.340 5.803 2.087 ATOM 41 H41 MOL 1 3.356 4.500 2.825 TER Here is the pdb format ; it is often used after calculations for the visualization . Good Work !! From wphoorn@utctu18.ct.utwente.nl Tue Sep 26 08:04:55 1995 Received: from ct.utwente.nl for wphoorn@utctu18.ct.utwente.nl by www.ccl.net (8.6.10/950822.1) id IAA06900; Tue, 26 Sep 1995 08:03:06 -0400 Received: from utctu18.ct.utwente.nl by ct.utwente.nl with SMTP id AA12755 (5.65c/IDA-1.4.4 for CHEMISTRY@www.ccl.net); Tue, 26 Sep 1995 13:01:33 +0100 Received: by utctu18.ct.utwente.nl (950511.SGI.8.6.12.PATCH526/940406.SGI.AUTO) id NAA20278; Tue, 26 Sep 1995 13:02:54 +0100 From: wphoorn@utctu18.ct.utwente.nl (Willem Paul van Hoorn) Message-Id: <199509261202.NAA20278@utctu18.ct.utwente.nl> Subject: Re: CCL:Formats of binary CHARMM files To: kostov@rainbow.uchicago.edu (Konstantin Kostov) Date: Tue, 26 Sep 1995 13:02:46 +0100 (MET) Cc: CHEMISTRY@www.ccl.net In-Reply-To: <9509252226.AA26119@rainbow.uchicago.edu> from "Konstantin Kostov" at Sep 25, 95 05:26:34 pm X-Mailer: ELM [version 2.4 PL5] Content-Type: text Content-Length: 1223 > > > Dear Netters, > > I need to read some binary files created with CHARMM. Could someone tell me > the formats of *.CRD, *.DCD and *.DVL files. > I would also appreciate any reference to existing programs that convert the > CHARMM binary files to ACSII. > The CHARMM manuals can be found at: http://www.ki.si/charmm/charmm.html The .CRD format is described under 'io.doc'. Normally this is an ascii file. As far as I remember binary files are machine dependent (at least the DCD and DVL files are). I don't know whether the other formats are described in these manuals. I remember that I have seen some description of these file formats, but maybe it was in the Quanta manuals. The CHARMM programs itself can convert binary files to ascii. Hope this helps, Willem Paul. ---------------------------------------------------------------------- (ir) Willem Paul van Hoorn University of Twente e-mail: wphoorn@ct.utwente.nl Laboratory of Organic Chemistry phone : (+31)53-892955 P.O. Box 217 (+31)53-892980 7500 AE Enschede, The Netherlands fax : (+31)53-312738 ---------------------------------------------------------------------- From erin@rani.chem.yale.edu Tue Sep 26 08:34:55 1995 Received: from rani.chem.yale.edu for erin@rani.chem.yale.edu by www.ccl.net (8.6.10/950822.1) id IAA07425; Tue, 26 Sep 1995 08:28:35 -0400 Received: by rani.chem.yale.edu; Tue, 26 Sep 95 08:28:34 -0400 From: Erin Duffy Message-Id: <9509261228.AA26534@rani.chem.yale.edu> Subject: CCL:Bend in DNA? To: chemistry@www.ccl.net Date: Tue, 26 Sep 95 8:28:34 EDT X-Mailer: ELM [version 2.3 PL11] Hi - I'm looking for a program that - given a set of coordinates - computes the bend in DNA helices. Someone indicated to me that a program called NEWHEL92 - apparently a product from Dickerson's group (?) - achieves this. If anyone has any information in this area and/or about this program, please reply to eduffy@laplace.csb.yale.edu. Thanks in advance. - Erin Duffy From arthur@csb0.IPC.PKU.EDU.CN Tue Sep 26 10:49:57 1995 Received: from csb0.IPC.PKU.EDU.CN for arthur@csb0.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/950822.1) id KAA10776; Tue, 26 Sep 1995 10:46:06 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@www.ccl.net id AA00083; Tue, 26 Sep 95 22:25:06 -0700 Date: Tue, 26 Sep 1995 22:25:05 -0700 (PDT) From: Arthur Wang To: CCL mailing list Subject: Ask Refs. for Combinatorial Chemistry Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I am not sure whether the Comp. Chem List is the right place to post such query, but I do need your help: Is there anyone who has experiences in combinatorial chemistry or anyone interested in it? I would appreciate it very much if you can provide a list of Refs. to me. Since I am really a beginner in this field, so everything with the subject "Combinatorial Chemistry" or "Combinatorial Library" is desired. ( Maybe you would cry out WHAT A STUPID STRATEGY! Yes. I think so too. In fact, I am right here ready to listen to your advices. ) Thank you for concern. Arthur Wang Peking University, Beijing arthur@ipc.pku.edu.cn From owner-chemistry@ccl.net Tue Sep 26 14:04:59 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id OAA15337; Tue, 26 Sep 1995 14:00:19 -0400 Received: from saturn.kent.edu for raeker@saturn.kent.edu by bedrock.ccl.net (8.6.10/950822.1) id OAA29085; Tue, 26 Sep 1995 14:00:16 -0400 Received: by saturn.kent.edu (AIX 3.2/UCB 5.64/4.03) id AA15556; Tue, 26 Sep 1995 13:47:08 -0400 Date: Tue, 26 Sep 1995 13:47:07 -0400 (EDT) From: "Todd J. Raeker" To: CCL Subject: HyperChem formation energy calculation Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII HyperChem users; I am using Hyperchem with pm3 to calculate heats of formation of a few cubane derivatives. Page 102 of the manual states that the heat of formation is calculated by subtracting atomic heats of formation from the total energies. I would like to look at these atomic heats of formation that HyperChem is using. Does anybody know the name of the file or a reference of where I might find these. I ask because the total energy appears to be O.K. but the reported heat of formation in the log file seems nonsense. I want to thoroughly check all aspects of this calculation. Thanks for any help. Dr. Todd J. Raeker | Department of Chemistry raeker@saturn.kent.edu | Kent State University Phone (216)-672-2986 | Kent, OH 44242-0001 From san@mbu.iisc.ernet.in Tue Sep 26 14:20:00 1995 Received: from soochak.ncst.ernet.in for san@mbu.iisc.ernet.in by www.ccl.net (8.6.10/950822.1) id OAA15741; Tue, 26 Sep 1995 14:19:06 -0400 Received: from mbu.iisc.ernet.in (mail.mbu.iisc.ernet.in [144.16.74.32]) by soochak.ncst.ernet.in (8.6.8.1/8.6.6) with ESMTP id WAA24719; Tue, 26 Sep 1995 22:49:46 +0530 Received: from mbu by mbu.iisc.ernet.in (ERNET-IISc/SMI-4.1) id WAA14459; Tue, 26 Sep 1995 22:41:07 -0700 Date: Tue, 26 Sep 1995 22:41:07 -0700 (PDT) From: Sandeep Kumar Bansal X-Sender: san@mbu To: Erin Duffy cc: "computational chem. list" Subject: Re: CCL:Bend in DNA? In-Reply-To: <9509261228.AA26534@rani.chem.yale.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Mr. Erin Duffy, you can contact Prof. Manju Bansal for program on DNA Bending. There is a program called NUPARM which does exactly what you want. You can get this program from PDB also. Prof. Bansals' email address is mb@mbu.iisc.ernet.in sandeep ******************************************************************************* SANDEEP KUMAR * Truly, as light manifests itself M.B.U., IISC. * and darkness, thus truth is the BANGALORE * standard of itself and of false. 560012 * INDIA * SPINOZA, Ethics, Pt II, Prop. 43. Phone 91-80-3092534 * email san@mbu.iisc.ernet.in * san@nova.mbu.iisc.ernet.in * ******************************************************************************* On Tue, 26 Sep 1995, Erin Duffy wrote: > Date: Tue, 26 Sep 95 8:28:34 EDT > From: Erin Duffy > To: chemistry@www.ccl.net > Subject: CCL:Bend in DNA? > > > Hi - I'm looking for a program that - given a set of coordinates - > computes the bend in DNA helices. Someone indicated to me > that a program called NEWHEL92 - apparently a product from > Dickerson's group (?) - achieves this. If anyone has any > information in this area and/or about this program, please > reply to eduffy@laplace.csb.yale.edu. Thanks in advance. > - Erin Duffy > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: erin@rani.chem.yale.edu > -- Original Sender From: Address: erin@rani.chem.yale.edu > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > From ipcakc@vigyan.iisc.ernet.in Tue Sep 26 18:35:03 1995 Received: from sangam.ncst.ernet.in for ipcakc@vigyan.iisc.ernet.in by www.ccl.net (8.6.10/950822.1) id SAA21441; Tue, 26 Sep 1995 18:26:53 -0400 From: Received: from iisc.ernet.in (iisc.iisc.ernet.in [144.16.64.3]) by sangam.ncst.ernet.in (8.6.12/8.6.6) with SMTP id DAA14708 for ; Wed, 27 Sep 1995 03:57:34 +0530 Received: from vigyan.UUCP by iisc.ernet.in (ERNET-IISc/SMI-4.1) id AA25163; Wed, 27 Sep 95 04:01:08+0530 Received: by vigyan.iisc.ernet.in (smail2.3) id AA09124; 26 Sep 95 13:12:08 EST (Tue) To: CHEMISTRY@www.ccl.net Subject: Tr.state for SiH_3+SiH_4--->SiH_4+SiH_3 reaction Date: 26 Sep 95 13:12:08 EST (Tue) Message-Id: <9509261312.AA09124@vigyan.iisc.ernet.in> I am trying to study a reaction of H-transfer between SiH_3 and SiH_4 leading to the same product (Thermoneutral reaction) in the doublet state. I am not able to obtain the transition state and could anyone suggest me any previous reference on this reaction? H_3Si + H---SiH_3 -------> H_3Si------H-------SiH_3 ----> H_3Si---H+SiH_3. reactant Symmetric Trn.State Product Thanks in advance, Sridhar ----------------------------------------------------------------------- Department of I.P.C., Indian Instt. of Science, Bangalore - 560 012, Inida. Fax : 080-3341683 Attn. Sridhar, IPC Ph. : 080-3344411 Extn. 2385. E-mail : ipcakc@vigyan.iisc.ernet.in Int.net: akc@hamsadvani.serc.iisc.ernet.in ------------------------------------------------------------------------ From CTARG@Levels.UniSA.Edu.Au Tue Sep 26 18:50:03 1995 Received: from LV.Levels.UniSA.Edu.Au for CTARG@Levels.UniSA.Edu.Au by www.ccl.net (8.6.10/950822.1) id SAA21569; Tue, 26 Sep 1995 18:40:40 -0400 From: Received: from Levels.UniSA.Edu.Au by Levels.UniSA.Edu.Au (PMDF V5.0-4 #9510) id <01HVRI9GSJTCKZEBGA@Levels.UniSA.Edu.Au> for chemistry@www.ccl.net; Wed, 27 Sep 1995 08:09:50 +0930 Date: Wed, 27 Sep 1995 08:09:50 +0930 Subject: parameters for NiO and CoO To: chemistry@www.ccl.net Message-id: <01HVRI9GWKHUKZEBGA@Levels.UniSA.Edu.Au> X-VMS-To: IN%"chemistry@www.ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Hi, A student and I have been trying to do a molecular modelling and atomic scale imaging project on NiO and CoO. This is proving to be extremely difficult for two reasons (a) we can't get any single crystals of these materials (b) we have been using ZINDO to do the molecular modelling part of the study and the results we have been getting are very odd. We have also tried the force field methodology MM+ but the resulting bond lengths are far to short, about 1.8A as compared to 2.1 in a NiO crystal. I know that atomic charges do not necessarily have a lot of meaning but the ZINDO methodology has given charges up to +6!! Two pleas for help - single crystals? - parameters for Ni or Co, these can be force field, semi-empirical, or ab-initio - I don't mind. At about this stage we are willing to try anything so any suggestions will be greatly appreciated! Thanks very much Andy. From owner-chemistry@ccl.net Tue Sep 26 22:50:06 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id WAA23795; Tue, 26 Sep 1995 22:38:56 -0400 Received: from utsc.s.u-tokyo.ac.jp for smori@chem.s.u-tokyo.ac.jp by bedrock.ccl.net (8.6.10/950822.1) id WAA03758; Tue, 26 Sep 1995 22:38:52 -0400 Received: from [133.11.6.102] (nakaquadra.chem.s.u-tokyo.ac.jp) by utsc.s.u-tokyo.ac.jp (5.67+1.6W/TISN-1.3/R2) id AA13914; Wed, 27 Sep 95 11:33:54 JST Message-Id: <9509270233.AA13914@utsc.s.u-tokyo.ac.jp> Date: Wed, 27 Sep 1995 11:37:38 +0900 To: chemistry@ccl.net From: smori@chem.s.u-tokyo.ac.jp (Mori Seiji) X-Sender: smori@chem.s.u-tokyo.ac.jp (Unverified) Subject: Please tell me a BSSE procedure with gaussian. Cc: smori@utsc.s.u-tokyo.ac.jp Mime-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) Dear Netters: (1) Would you tell me the procedure of the estimation of BSSE by G92 or G94? Could they compute this? I will be happy if you send also an example of input file. Additionally, I would like to use general basis sets in a input stream in this calculation. Thanks for advance. Sincerely yours, Seiji Mori ============================(^-^)=========================== Seiji Mori Nakamura Lab. Department of Chemistry The University of Tokyo Tel: 03-3812-2111 ext.4647 FAX: 03-5800-6889 Address: 7-3-1, Hongou, Bunkyo-ku, Tokyo 113, JAPAN email: smori@chem.s.u-tokyo.ac.jp