From chemistry-request@server.ccl.net Fri May 28 05:25:05 1999 Received: from lgsx01.lg.ehu.es (lgsx01.lg.ehu.es [158.227.2.34]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id FAA25577 for ; Fri, 28 May 1999 05:24:32 -0400 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by lgsx01.lg.ehu.es (8.8.5/8.8.5) with SMTP id LAA06322; Fri, 28 May 1999 11:04:02 +0200 (MET DST) Date: Fri, 28 May 1999 11:01:22 +0200 (MET DST) From: Pablo Vitoria Garcia To: Gavin Tsai cc: CHEMISTRY@ccl.net Subject: Re: CCL:Ahlrich's VTZ basis set In-Reply-To: <374D8D53.E3899DE1@po.cwru.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Gavin, Try ftp.chemie.uni-karlsruhe.de under pub/basen. You'll find there a file for each element with SV, DZ, TZV, polarization functions,... Best regards Pablo On Thu, 27 May 1999, Gavin Tsai wrote: > Hi, CCLers: > > I tried to download Ahlrich's VTZ basis set from > tchibm3.chemie.uni-karlsruhe.de which they allowed anonymous logging. > Unfortunately, the anonymous is rejected. The VTZ basis set also does > not list on his 1992 JCP paper. Any help would be appreciated!! > > Gavin Tsai > -------------------------------------------------------------------------------- Pablo Vitoria Garcia Departamento de Quimica Inorganica, Facultad de Ciencias Universidad del Pais Vasco (UPV/EHU) Apartado 644, E-48080 Bilbao SPAIN e-mail: qibvigap@lg.ehu.es Phone: +34 94 6012000 Ext. 5529 -------------------------------------------------------------------------------- From chemistry-request@server.ccl.net Fri May 28 06:38:48 1999 Received: from chris2.u-strasbg.fr (maerker@chris2.u-strasbg.fr [130.79.34.140]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id GAA26330 for ; Fri, 28 May 1999 06:38:46 -0400 Received: (from maerker@localhost) by chris2.u-strasbg.fr (8.8.8/8.8.8) id MAA02075; Fri, 28 May 1999 12:34:41 +0200 From: Christoph Maerker Message-Id: <199905281034.MAA02075@chris2.u-strasbg.fr> Subject: G98: pcm charge errors To: chemistry@ccl.net (ccl) Date: Fri, 28 May 1999 12:34:41 +0200 (MEST) Cc: maerker@chris2.u-strasbg.fr (Christoph Maerker) Organization: Laboratoire de Chimie Biophysique Institut Le Bel Universite Louis Pasteur Postal-Address: 4, rue Blaise Pascal, F- 67000 Strasbourg FRANCE Phone: +33/3-88-41-53-19 Fax: +33/3-88-60-63-83 A tous, I do some PCM single point calculations with G98. In the output file I find notes like the following one: Error on NUCLEAR pol.charges = 0.80860 Error on ELECTR. pol.charges =-1.00268 An "error" of about one unit charge seems quite a lot to me. 1) How does this error affect computed solvation (free) energies, I mean how reliable are these values ? 2) Is there a rule of thumb to which magnitude errors in polarisation charges are acceptable ? 3) Are there keywords or keyword options by which one can reduce such charge errors ? By the way, I noticed that these charge errors depend on the solvation model chosen. Empirically the COSMO implementation (i.e. cpcm) often has smaller charge errors than dpcm, but there are exceptions too. I will summarize to the list. Amicalement, Christoph From chemistry-request@server.ccl.net Fri May 28 08:51:39 1999 Received: from csb0.IPC.PKU.EDU.CN (csb0.ipc.pku.edu.cn [162.105.177.12]) by server.ccl.net (8.8.7/8.8.7) with SMTP id IAA27898 for ; Fri, 28 May 1999 08:51:33 -0400 Received: by csb0.IPC.PKU.EDU.CN (920330.SGI/940406.SGI.AUTO) for chemistry@ccl.net id AA09702; Fri, 28 May 99 20:47:32 -0700 Date: Fri, 28 May 1999 20:47:31 -0700 (PDT) From: Liu Zhijie To: chemistry@ccl.net Subject: About Charmm Minimization In-Reply-To: <000701bea356$a252c180$d29a4e81@pc146> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear all, When I use CHARMM97 to minimize the protein structures, coordinates of the water molecules (include associated water and solvent water ) and the metal ions can not be setup and read in. Since the topology files AMINO.BIN and IONS.RTF include these segments , there may are some problems in my input file. Please examine the head of my input file and give your oppinions, any help will be appreciate. ------------------------------------------------------- BOML -1 | | OPEN READ UNIT 11 FILE NAME "$CHM_DATA/AMINO.BIN" | READ RTF UNIT 11 FILE | CLOSE UNIT 11 | | OPEN READ UNIT 12 FILE NAME "$CHM_DATA/PARM.BIN" | READ PARAMETERS UNIT 12 FILE | CLOSE UNIT 12 | | OPEN READ UNIT 13 CARD NAME "$CHM_DATA/IONS.RTF" | READ PARAMETERS UNIT 13 CARD | CLOSE UNIT 13 | | OPEN READ UNIT 14 CARD NAME x.pdb | READ SEQUENCE PDB UNIT 14 | | GENERATE XXXX SETUP | | REWIND UNIT 14 | | READ COORDINATES PDB UNIT 14 | CLOSE UNIT 14 | ------------------------------------------------------- Sincerely yours Liu Zhijie ********************************************************************** Chinese Name: Zhijie Liu * English Name : Elmer ********************************************************************** MOLECULAR DESIGN LABORATORY *** TEL : 8610-62751490 (LAB ) INSTITUTE OF PHYSICAL CHEMISTRY *** 8610-62754032-324 (DORM) PEKING UNIVERSITY *** FAX : 8610-62751725 BEIJING 100871 , P.R.CHINA *** EMAIL : lzj@ipc.pku.edu.cn ********************************************************************** ADDRESS: BUILDING 39* ROOM 324 * PEKING UNIVERSITY* 100871* P.R.CHINA ********************************************************************** From chemistry-request@server.ccl.net Fri May 28 10:13:16 1999 Received: from gandalf.ciam.unibo.it (gandalf.ciam.unibo.it [137.204.214.21]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA29801 for ; Fri, 28 May 1999 10:13:14 -0400 Received: from localhost.0.0.127.in-addr.arpa by gandalf.ciam.unibo.it (AIX 3.2/UCB 5.64/4.03) id AA19079; Fri, 28 May 1999 16:02:49 +0100 Sender: luca@gandalf.ciam.unibo.it Message-Id: <374EB018.59E2@uniroma1.it> Date: Fri, 28 May 1999 16:02:48 +0100 From: Luca Schiaffino Organization: Universita' "La Sapienza" X-Mailer: Mozilla 3.0 (X11; I; AIX 2) Mime-Version: 1.0 To: chemistry@ccl.net Subject: Problems with the UFF in Gaussian 98 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We have experienced some problems when performing geometry optimizations with the Universal Force Field (UFF) as implemented in Gaussian 98: single point calculations on minimum energy structures result in energies very much lower than the final one of the optimization. Moreover, reoptimization of these structures leads to a very different geometry, with an energy lower than that of the starting structure. This strange behaviour is very evident in the case of large molecules or complexes, and appears to be absent in the case of small molecules. We suspect that this problem is related to the evaluation of partial charges and/or electrostatic interactions: - when the keyword iop(4/67=2) is included in the input file, the program does not assign partial charges (consequently we obtain a zero dipole moment even for highly unsymmetrical molecules) and electrostatic interactions are not evaluated (i.e. they are all zero). In this case we do not experience any problem and reoptimization of minimum energy structures leads to the input geometry. - when the keyword iop(4/67=221) is included, the program assigns partial charges to all atoms and we experience the problems mentioned above. - when we specify the partial charges in the input file (i.e. the program does not assign partial charges, but evaluates electrostatic interactions by using the ones we have specified), we do not experience any problem and again reoptimization of minimum energy structures leads to the input geometry. Of course, we observe the same problems even when we use UFF for the lower layer in ONIOM calculations and for this reason we have not yet been able to obtain minimum energy structures of large molecules with the use of ONIOM method. We would like to know is someone else has experienced the same problems. Greetings Dr. Luca Schiaffino Dipartimento di Chimica Universita' di Roma "La Sapienza" e-mail: lschiaffino@uniroma1.it From chemistry-request@server.ccl.net Fri May 28 10:53:29 1999 Received: from SEMOVM.SEMO.EDU (semovm.semo.edu [150.201.1.1]) by server.ccl.net (8.8.7/8.8.7) with SMTP id KAA30770 for ; Fri, 28 May 1999 10:53:29 -0400 Received: from tony [150.201.19.145] by SEMOVM.SEMO.EDU (IBM VM SMTP V2R4a) via TCP with SMTP ; Fri, 28 May 1999 09:46:25 CDT Message-Id: <3.0.5.32.19990528095000.007b7100@semovm.semo.edu> X-Sender: ajduben@semovm.semo.edu X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Fri, 28 May 1999 09:50:00 -0500 To: chemistry@ccl.net From: "Anthony J. Duben" Subject: Average conformations Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Here is a copy, more or less, of a communication I sent to Richard Wood directly in response to his original question about determining an average conformation: I think that you would need to have a Boltzmann distribution of conformations over which you would need to average. The problem with calculating average conformations is finding average angles and properties that depend on average angles (e.g., J coupling constants). Since angles are re-entrant, you need to be really careful. As pointed out earlier in this thread, an angle of 60 degrees and an angle of -60 degrees do not average to 0. To make matters worse, the averaging depends on the origin of the angle system. If one uses 300 degrees instead of -60, you get an average of 180. Here are a couple of references in which I present some ideas on angle averaging. The second is probably hard to find since it is in a Proceedings volume. I will send a copy to anyone who wants one. In it I demonstrate how it is possible to average angles while preserving rotational invariance. Anthony J. Duben, Milos Hricovini, Igor Tvaroska, "The conformational analysis of methyl beta-xylobioside: effect of choice of potential functions" Carbohydrate Research, vol. 247 (1993), pp 71 - 81 Anthony J. Duben "Angle Averaging Procedures in the Conformational Analysis of Polymers", Proceedings of the Summer Computer Simulation Conference 1989, pp. 310 - 314 Anthony J. Duben (ajduben@semovm.semo.edu) Anthony J. Duben Professor, Computer Science Dept., MS 5950 and Associate Dean, College of Science and Technology, MS 6000 Southeast Missouri State University 1 University Plaza Cape Girardeau MO 63701-4799 phone: 573-986-6036 [Dean's Office] 573-651-2194 [Computer Science Dept.] fax: 573-651-2223 [Dean's Office] 573-651-2791 [Computer Science Dept.] e-mail: ajduben@semovm.semo.edu c867buc@semovm.semo.edu "Education is not the filling of a pail but the lighting of a fire." -- William Butler Yeats From chemistry-request@server.ccl.net Fri May 28 10:54:16 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA30797 for ; Fri, 28 May 1999 10:54:16 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id KAA03621; Fri, 28 May 1999 10:49:44 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <374EAE39.A5F6DD32@syr.edu> Date: Fri, 28 May 1999 10:54:49 -0400 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: Liu Zhijie CC: chemistry@ccl.net Subject: Re: CCL:About Charmm Minimization References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear LIu, You should read in the second RTF before reading in the parameters. Also the read command for ions.rtf should be read rtf and NOT read para. It should be READ RTF UNIT 13 CARD APPEND\ Regards Deepak. Liu Zhijie wrote: > Dear all, > > When I use CHARMM97 to minimize the protein structures, coordinates > of the water molecules (include associated water and solvent water ) and > the metal ions can not be setup and read in. > Since the topology files AMINO.BIN and IONS.RTF include these > segments , there may are some problems in my input file. Please examine > the head of my input file and give your oppinions, any help will be > appreciate. > > ------------------------------------------------------- > BOML -1 | > | > OPEN READ UNIT 11 FILE NAME "$CHM_DATA/AMINO.BIN" | > READ RTF UNIT 11 FILE | > CLOSE UNIT 11 | > | > OPEN READ UNIT 12 FILE NAME "$CHM_DATA/PARM.BIN" | > READ PARAMETERS UNIT 12 FILE | > CLOSE UNIT 12 | > | > OPEN READ UNIT 13 CARD NAME "$CHM_DATA/IONS.RTF" | > READ PARAMETERS UNIT 13 CARD | > CLOSE UNIT 13 | > | > OPEN READ UNIT 14 CARD NAME x.pdb | > READ SEQUENCE PDB UNIT 14 | > | > GENERATE XXXX SETUP | > | > REWIND UNIT 14 | > | > READ COORDINATES PDB UNIT 14 | > CLOSE UNIT 14 | > ------------------------------------------------------- > Sincerely yours > > Liu Zhijie > > ********************************************************************** > Chinese Name: Zhijie Liu * English Name : Elmer > ********************************************************************** > MOLECULAR DESIGN LABORATORY *** TEL : 8610-62751490 (LAB ) > INSTITUTE OF PHYSICAL CHEMISTRY *** 8610-62754032-324 (DORM) > PEKING UNIVERSITY *** FAX : 8610-62751725 > BEIJING 100871 , P.R.CHINA *** EMAIL : lzj@ipc.pku.edu.cn > ********************************************************************** > ADDRESS: BUILDING 39* ROOM 324 * PEKING UNIVERSITY* 100871* P.R.CHINA > ********************************************************************** > > -= 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 -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry & Biochemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Fri May 28 11:46:14 1999 Received: from judy.ic.ac.uk (judy.ic.ac.uk [155.198.5.28]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA31971 for ; Fri, 28 May 1999 11:46:13 -0400 Received: from juliet.ic.ac.uk ([155.198.5.4]) by judy.ic.ac.uk with esmtp (Exim 2.12 #1) id 10nOmK-0000Bh-00 for chemistry@ccl.net; Fri, 28 May 1999 15:42:36 +0000 Received: from icex5.cc.ic.ac.uk ([155.198.3.5]) by juliet.ic.ac.uk with esmtp (Exim 2.12 #1) id 10nOmF-00070k-00 for chemistry@ccl.net; Fri, 28 May 1999 15:42:31 +0000 Received: by icex5.cc.ic.ac.uk with Internet Mail Service (5.5.2448.0) id ; Fri, 28 May 1999 16:42:30 +0100 Message-ID: From: "Hogg, S.E." To: "'chemistry@ccl.net'" Subject: rdf - Radial Distribution Function Date: Fri, 28 May 1999 16:42:27 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2448.0) Content-Type: text/plain Is there a nice (free???) software package that wil examine a repeat unit structure and output the rdf for selected atoms (or atom types)? I have a glass structure and want to calculate the rdf to see if it matches 'literature' values. -- Simon Hogg From chemistry-request@server.ccl.net Fri May 28 11:50:29 1999 Received: from mailbox.syr.edu (root@mailbox.syr.edu [128.230.18.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA32110 for ; Fri, 28 May 1999 11:50:28 -0400 Received: from syr.edu (curie.syr.edu [128.230.187.116]) by mailbox.syr.edu (8.9.2/8.9.2) with ESMTP id LAA20864; Fri, 28 May 1999 11:46:16 -0400 (EDT) Sender: desingh@mailbox.syr.edu Message-ID: <374EBB79.796C9E9B@syr.edu> Date: Fri, 28 May 1999 11:51:21 -0400 From: Deepak Singh Organization: Dept. of Chem & Biochem, Syracuse University X-Mailer: Mozilla 4.07C-SGI [en] (X11; I; IRIX64 6.5 IP30) MIME-Version: 1.0 To: Liu Zhijie , chemistry@ccl.net Subject: Re: CCL:About Charmm Minimization References: <374EAE39.A5F6DD32@syr.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit There is a slight ypo in my message ... Ignore the \ after "APPEND" Deepak. Deepak Singh wrote: > Dear LIu, > > You should read in the second RTF before reading in the parameters. Also the read > command for ions.rtf should be read rtf and NOT read para. It should be > > READ RTF UNIT 13 CARD APPEND\ > > Regards > > Deepak. > > Liu Zhijie wrote: > > > Dear all, > > > > When I use CHARMM97 to minimize the protein structures, coordinates > > of the water molecules (include associated water and solvent water ) and > > the metal ions can not be setup and read in. > > Since the topology files AMINO.BIN and IONS.RTF include these > > segments , there may are some problems in my input file. Please examine > > the head of my input file and give your oppinions, any help will be > > appreciate. > > > > ------------------------------------------------------- > > BOML -1 | > > | > > OPEN READ UNIT 11 FILE NAME "$CHM_DATA/AMINO.BIN" | > > READ RTF UNIT 11 FILE | > > CLOSE UNIT 11 | > > | > > OPEN READ UNIT 12 FILE NAME "$CHM_DATA/PARM.BIN" | > > READ PARAMETERS UNIT 12 FILE | > > CLOSE UNIT 12 | > > | > > OPEN READ UNIT 13 CARD NAME "$CHM_DATA/IONS.RTF" | > > READ PARAMETERS UNIT 13 CARD | > > CLOSE UNIT 13 | > > | > > OPEN READ UNIT 14 CARD NAME x.pdb | > > READ SEQUENCE PDB UNIT 14 | > > | > > GENERATE XXXX SETUP | > > | > > REWIND UNIT 14 | > > | > > READ COORDINATES PDB UNIT 14 | > > CLOSE UNIT 14 | > > ------------------------------------------------------- > > Sincerely yours > > > > Liu Zhijie > > > > ********************************************************************** > > Chinese Name: Zhijie Liu * English Name : Elmer > > ********************************************************************** > > MOLECULAR DESIGN LABORATORY *** TEL : 8610-62751490 (LAB ) > > INSTITUTE OF PHYSICAL CHEMISTRY *** 8610-62754032-324 (DORM) > > PEKING UNIVERSITY *** FAX : 8610-62751725 > > BEIJING 100871 , P.R.CHINA *** EMAIL : lzj@ipc.pku.edu.cn > > ********************************************************************** > > ADDRESS: BUILDING 39* ROOM 324 * PEKING UNIVERSITY* 100871* P.R.CHINA > > ********************************************************************** > > > > -- > ********************************************************************** > Deepak Singh Tel : (315)443 1739 (w) > Graduate Student (315)472 9659 (h) > Dept. of Chemistry & Biochemistry Fax : (315)443 4070 > Syracuse University email : desingh@syr.edu > 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh > NY 13244 > > "Violence is the last refuge of the incompetent." --- Salvor Hardin > ********************************************************************** > > -= 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 -- ********************************************************************** Deepak Singh Tel : (315)443 1739 (w) Graduate Student (315)472 9659 (h) Dept. of Chemistry & Biochemistry Fax : (315)443 4070 Syracuse University email : desingh@syr.edu 1-014 CST, Syracuse URL : http://web.syr.edu/~desingh NY 13244 "Violence is the last refuge of the incompetent." --- Salvor Hardin ********************************************************************** From chemistry-request@server.ccl.net Fri May 28 13:46:09 1999 Received: from dfw7-1.relay.mail.uu.net (dfw7-1.relay.mail.uu.net [199.171.54.106]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA00960 for ; Fri, 28 May 1999 13:46:09 -0400 Received: from uucp1.uu.net by dfw7sosrv11.alter.net with SMTP (peer crosschecked as: uucp1.uu.net [192.48.96.81]) id QQgrek13102 for ; Fri, 28 May 1999 17:42:32 GMT Message-Id: Received: from m10.UUCP by uucp1.uu.net with UUCP/RMAIL ; Fri, 28 May 1999 13:42:07 -0400 Received: by m10.lorentzian.com; Fri, 28 May 1999 11:39:21 -0400 Received: by mousse.gaussian.com; Fri, 28 May 1999 12:12:13 -0400 From: gaussian.com!janocha@lorentzian.com (Wendy Janocha) Subject: Special Events for Gaussian User Community: Workshop and User's Group To: chemistry@ccl.net Date: Fri, 28 May 1999 12:12:13 -0400 (EDT) X-Mailer: ELM [version 2.4 PL24] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit We are pleased to announce two events of special interest to the Gaussian user community, a four day workshop to be held at CINECA in Bologna, Italy July 26-29, 1999 and a one-day user's group meeting to be help in conjunction with WATOC on July 31, 1999 in London, England. The workshop is being sponsored by SGI and CINECA and will cover the full range of Gaussian functionality including theory, practical approaches, and substantial hands-on time. You can request registration information either via E-mail to info@gaussian.com or at the web site, http://www.cineca.it. The User's Group meeting will be held at Imperial College and will include presentations on research using Gaussian by Prof. Ken Houk, tutorials on the ONIOM methods and the CBS model chemistries, and recent developments in prediction of molecular properties by Prof. Vincenzo Barone. It will also include substantial time for open question and answer sessions with the Gaussian developers. Wendy G. Janocha General Manager janocha@gaussian.com http://www.gaussian.com