From pino@jsbach.dichi.unina.it Wed May 21 10:43:46 1997 Received: from jsbach.dichi.unina.it for pino@jsbach.dichi.unina.it by www.ccl.net (8.8.3/950822.1) id KAA05799; Wed, 21 May 1997 10:15:31 -0400 (EDT) From: Received: by jsbach.dichi.unina.it (AIX 3.2/UCB 5.64/4.03) id AA12594; Thu, 15 Feb 1996 16:09:42 +0100 Date: Thu, 15 Feb 1996 16:09:42 +0100 Message-Id: <9602151509.AA12594@jsbach.dichi.unina.it> To: chemistry@www.ccl.net Subject: AM1 frequencies scaling I would appreciate to receive information about scaling of AM1 frequencies ===================== Giuseppe Milano Universita' degli Studi di Napoli pino@jsbach.dichi.unina.it ===================================0 From Jeffrey.Nauss@UC.Edu Wed May 21 11:43:48 1997 Received: from blues.fd1.uc.edu for Jeffrey.Nauss@UC.Edu by www.ccl.net (8.8.3/950822.1) id LAA06397; Wed, 21 May 1997 11:38:09 -0400 (EDT) Received: from beryllium.crs.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-7 #15949) id <01IJ4OX9UH9OHMAIR9@UCBEH.SAN.UC.EDU> for chemistry@www.ccl.net; Wed, 21 May 1997 11:36:55 -0500 (EST) Received: by beryllium.crs.uc.edu (950413.SGI.8.6.12/940406.SGI.AUTO) for chemistry@www.ccl.net id LAA02400; Wed, 21 May 1997 11:37:46 -0400 Date: Wed, 21 May 1997 11:37:46 -0400 From: Jeffrey.Nauss@UC.Edu (Jeffrey L. Nauss) Subject: Spartan: MM2 parameters problems To: chemistry@www.ccl.net Reply-to: Jeffrey.Nauss@UC.Edu Message-id: <9705211137.ZM2398@beryllium.crs.uc.edu> Organization: Dept. Chemistry, University of Cincinnati MIME-version: 1.0 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Zm-Priority: Low We have a student here using Sparatan to examine silarylene siloxanes. He has no problem when carbon is substituted for the silicons. However, when he includes the silicone atoms, he gets the following in the output file: SPARTAN MECHANICS (MM2) PROGRAM: SGI/R4K Release 4.1 a2 (Job run on ucmodl.che.uc.edu) test Missing angle parameter: 2 19 6 0 (2 1 13) Not being familiar with Spartan, I cannot make any sense out of this error message. I suspect that some valance bond angle parameter is missing for the silicon atom but which one? Looking in the params.MM2 I do not see any indication of what atoms correspond to which set of parameters. Any suggestions will be helpful. Thank you in advance. -- Jeffrey L. Nauss, PhD Telephone: 513-556-0148 Dir. Molec. Model. Serv. Fax: 513-556-9239 Department of Chemistry e-mail: Jeffrey.Nauss@UC.Edu University of Cincinnati URL http://www.che.uc.edu/~nauss From boufer@cennas.nhmfl.gov Wed May 21 12:43:48 1997 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id MAA06681; Wed, 21 May 1997 12:28:39 -0400 (EDT) Received: from localhost (boufer@localhost) by cennas.nhmfl.gov (8.8.5/8.8.5) with SMTP id MAA15121 for ; Wed, 21 May 1997 12:28:38 -0400 (EDT) Date: Wed, 21 May 1997 12:28:38 -0400 (EDT) From: Ahmed Bouferguene X-Sender: boufer@cennas To: chemistry@www.ccl.net Subject: G-92 : About massive charges. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, I apologize for my previous question regarding "a restless massive charge" which was incomplete. To be more specific, I am looking for an option in g-92 allowing to calculate the energy of a system in the field of a moving charge (R varies with a predefined step-size) and where the center of mass is the orgin of the coordinate system (for each R, the center of mass moves to a new position). Thanks. From joe@mickey.chem.luc.edu Wed May 21 12:55:10 1997 Received: from mickey.chem.luc.edu for joe@mickey.chem.luc.edu by www.ccl.net (8.8.3/950822.1) id MAA06568; Wed, 21 May 1997 12:01:42 -0400 (EDT) Received: by mickey.chem.luc.edu (940816.SGI.8.6.9/940406.SGI.AUTO) for chemistry@www.ccl.net id LAA12229; Wed, 21 May 1997 11:13:41 -0700 From: joe@mickey.chem.luc.edu (Joseph S Brunzelle) Message-Id: <9705211113.ZM12227@mickey.chem.luc.edu> Date: Wed, 21 May 1997 11:13:36 -0700 X-Mailer: Z-Mail (3.2.0 26oct94 MediaMail) To: chemistry@www.ccl.net Subject: transition state calcul Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi everyone !! I have been trying to do a ts calculation within spartan and I've actually have results. The only problem is that I don't know exactly how to best interpet them in relation to what is a possible ts. Does anyone know of some good references ranging from easy to more complex material. This would help me understand and allow me to perform a more accurate calculation. Also if there is advice for the use of the ts calculation within spartan, it would be great. Thank you in advance!!! Please respond to joe@mickey.chem.luc.edu, I will post a summary once I receive the info. -- ------------------------------------------------------------------------ Joseph S. Brunzelle (joe@mickey.chem.luc.edu) Loyola University of Chicago Dept. of Chemistry Chicago, IL 60626 Tel. 773-508-3132 Fax. 773-508-3086 ------------------------------------------------------------------------- From beroza@scripps.edu Wed May 21 13:01:01 1997 Received: from relay1.scripps.edu for beroza@scripps.edu by www.ccl.net (8.8.3/950822.1) id MAA06723; Wed, 21 May 1997 12:37:36 -0400 (EDT) Received: from euler.scripps.edu (euler.scripps.edu [137.131.252.34]) by relay1.scripps.edu (8.8.5/TSRI-1.5) with ESMTP id JAA08973 for ; Wed, 21 May 1997 09:37:35 -0700 (PDT) Received: (from beroza@localhost) by euler.scripps.edu (8.8.5/TSRI-1.4) id JAA28032 for chemistry@www.ccl.net; Wed, 21 May 1997 09:37:10 -0700 (PDT) Date: Wed, 21 May 1997 09:37:10 -0700 (PDT) From: Paul Beroza Message-Id: <199705211637.JAA28032@euler.scripps.edu> To: chemistry@www.ccl.net Subject: mapping sequence data onto know 2ndary structures A couple of weeks ago Dan Severance wrote: > I want to be able to quickly generate a given secondary structure > from a sequence, and I'd like to do it nongraphically so I can generate > a large number with little or no "human" intervention :-) > I'm not talking reality, per se, just a sequence and an identifier > of some sort specifying that I want a generic beta sheet, gamma turn, > etc. > I know how to do it graphically in various software packages, but > I want to be able to generate these from an automated script. I wrote a program, "peptide", to do this. It is in the NAB language (which was designed for nucleic acids, but can also be used for proteins) The command line syntax is: % peptide structure sequence < -lib libfile> where "structure" defines the type of structure to be created and "sequence" is a string o of 1 letter amino acid codes. For example: % peptide ALPHA AAAAA -lib conf.lib will write out (in pdb format) the coordinates of an alanine pentapeptide in an alpha helical structure. You must have the "nab" compiler: info on nab = http://www.scripps.edu/case. nab source = ftp://ftp.scripps.edu/pub/macke/nab-2.1.tar.Z Once you have the nab compiler installed, get the peptide package from ftp://ftp.scripps.edu/pub/beroza/peptide I hope this is useful, and any comments and suggestions about the program are welcome. Paul --------------------------------------------------------------------- Paul Beroza The Scripps Research Institute email: beroza@scripps.edu Department of Molecular Biology phone: 619-784-9957 10550 N. Torrey Pines Rd. - TPC15 fax: 619-784-8896 La Jolla, CA 92037 URL: www.scripps.edu/~beroza --------------------------------------------------------------------- From cxy13@roo.INS.CWRU.Edu Wed May 21 16:43:50 1997 Received: from roo.INS.CWRU.Edu for cxy13@roo.INS.CWRU.Edu by www.ccl.net (8.8.3/950822.1) id QAA07919; Wed, 21 May 1997 16:10:57 -0400 (EDT) Received: (cxy13@localhost) by roo.INS.CWRU.Edu (8.7.6+cwru/CWRU-2.3-bsdi) id QAA23365; Wed, 21 May 1997 16:10:57 -0400 (EDT) (from cxy13) Message-Id: <199705212010.QAA23365@roo.INS.CWRU.Edu> Date: Wed, 21 May 1997 16:10:57 -0400 (EDT) From: cxy13@po.CWRU.Edu (Chia-Ning Yang) To: chemistry@www.ccl.net Subject: Conv=N command in G94 Reply-To: cxy13@po.CWRU.Edu (Chia-Ning Yang) Hello, I happen to forget where to put the command Conver=N in g94 input file. Can somebody answer me this? Thanks. C. Yang From berriz@chasma.harvard.edu Wed May 21 17:43:52 1997 Received: from chasma.harvard.edu for berriz@chasma.harvard.edu by www.ccl.net (8.8.3/950822.1) id RAA08295; Wed, 21 May 1997 17:39:10 -0400 (EDT) Received: by chasma.harvard.edu (AIX 3.2/UCB 5.64/4.03) id AA19149; Wed, 21 May 1997 17:35:42 -0400 Date: Wed, 21 May 1997 17:35:42 -0400 From: berriz@chasma.harvard.edu (Gabriel Berriz) Message-Id: <9705212135.AA19149@chasma.harvard.edu> To: chemistry@www.ccl.net Subject: Stochastic dynamics & "reduced atoms" Keywords: "reduced-atom" representations, stochastic dynamics Dear Netters: I am a graduate student in biophysics interested in reading about the use of "reduced atom" or ("reduced molecule") representations(*) in stochastic dynamics simulations, and in particular, any discussion on dealing with the distortions in conformational sampling produced by reduced representations. (Can one improve the quality of the sampling in a reduced representation model by modifying the statistical features of the noise term in the classical Langevin equation?) I would appreciate your suggestions for readings on this subject. Thank you very much, G. Berriz berriz@chasma.harvard.edu (*) P.S. Just in case my terminology is not entirely correct or standard, I will spell out in more detail what I mean. I would like to (eventually) perform stochastic dynamics simulations of long (model) polymer chains. Since I am interested in long time scales, I must keep the molecules' representation, as well as the mechanism for simulating the stochastic component of the dynamics, as simple as possible. For this reason, I would like to use some form of "reduced atom" representation. For example, instead of representing a methyl group by its carbon and three attached hydrogens, one can represent the whole group by a heavier mass concentrated at their center of mass. Alternatively, one can keep all four atoms, but instead of applying random forces to all of them (this representing the noise term of the stochastic equation of motion), one could apply only a random torque around the bond connecting the methyl group to the rest of the molecule (and treat the rest of the methyl group as rigid). Another common "reduced atom" representation is the C-alpha-C-alpha pseudo-bond representation of proteins proposed many years ago by Flory. One possible objection to these reduced representations is that their sampling of conformational space does not correspond sufficiently closely to the sampling performed by the fully represented molecule. As a trivial example of this, the reduced pseudo-bond representation of a tripeptide, where only the C-alpha carbons are moved randomly (subject only pseudo-bond length constraints), allows a considerably greater range for the C-alpha-C-alpha-C-alpha angle, than does the full representation of the tripeptide (with its corresponding constraints). From jmartell@uoguelph.ca Wed May 21 18:43:50 1997 Received: from ccshst09.cs.uoguelph.ca for jmartell@uoguelph.ca by www.ccl.net (8.8.3/950822.1) id RAA08628; Wed, 21 May 1997 17:44:20 -0400 (EDT) Received: from ccshst01.cs.uoguelph.ca by ccshst09.cs.uoguelph.ca with ESMTP (1.40.112.3/16.2) id AA027511061; Wed, 21 May 1997 17:44:21 -0400 Received: from localhost by ccshst01 with SMTP (1.37.109.20/16.2) id AA173471061; Wed, 21 May 1997 17:44:21 -0400 Date: Wed, 21 May 1997 17:44:21 -0400 (EDT) From: Jaime Martell X-Sender: jmartell@ccshst01 To: Chia-Ning Yang Cc: chemistry@www.ccl.net Subject: Re: CCL:G:Conv=N command in G94 In-Reply-To: <199705212010.QAA23365@roo.INS.CWRU.Edu> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 21 May 1997, Chia-Ning Yang wrote: > Hello, > I happen to forget where to put the command Conver=N in > g94 input file. Can somebody answer me this? > Thanks. > C. Yang > Wherever the G94 manual tells you to put it. My apology if you don't have a manual, but doesn't Gaussian still supply them with every purchase? It just seems to me that a large portion of the questions asked here could better be answered by searching in manuals, or calling or e-mailing the appropriate help desk (Gaussian or whomever is your favourite software vendor). Jaime Martell, Ph.D. Phone: (519) 824-4120 Ext. 8520 Department of Chemistry & Biochemistry E-mail: jmartell@uoguelph.ca University of Guelph Guelph, Ontario, Canada N1G 2W1 From huang@nissan.wavefun.com Wed May 21 18:54:54 1997 Received: from volvo.wavefun.com for huang@nissan.wavefun.com by www.ccl.net (8.8.3/950822.1) id SAA08757; Wed, 21 May 1997 18:07:05 -0400 (EDT) Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@www.ccl.net id AA28561; Wed, 21 May 97 15:08:57 -0700 Received: from nissan.wavefun.com(198.147.95.2) by volvo.wavefun.com via smap (V1.3) id sma028557; Wed May 21 15:07:36 1997 Received: by nissan.wavefun.com (931110.SGI/940406.SGI.AUTO) for @volvo.wavefun.com:chemistry@www.ccl.net id AA09267; Wed, 21 May 97 15:03:48 -0700 From: "Wayne Huang" Message-Id: <9705211503.ZM9265@nissan.wavefun.com> Date: Wed, 21 May 1997 15:03:38 -0700 In-Reply-To: joe@mickey.chem.luc.edu (Joseph S Brunzelle) "CCL:transition state calcul" (May 21, 11:13am) References: <9705211113.ZM12227@mickey.chem.luc.edu> Reply-To: huang@wavefun.com X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) To: joe@mickey.chem.luc.edu (Joseph S Brunzelle) Subject: Re: CCL:transition state calcul Cc: chemistry@www.ccl.net Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii On May 21, 11:13am, Joseph S Brunzelle wrote: > Subject: CCL:transition state calcul > Hi everyone !! > I have been trying to do a ts calculation within spartan and I've > actually have results. The only problem is that I don't know exactly how to > best interpet them in relation to what is a possible ts. Does anyone know of > some good references ranging from easy to more complex material. This would > help me understand and allow me to perform a more accurate calculation. Also > if there is advice for the use of the ts calculation within spartan, it would > be great. There are a few general references there dealing with transition state modeling. Warren Hehre's "Practical Strategies for Electronic Structure Calculations" has a chapter devoted for obtaining TS and verifying reaction path. The easy way to identify a specific TS is to run a frequency calculation on the optimized structure and animate the one and only one imaginary mode and see what reaction of this normal mode correponds to. Moreover, I am working a project of archiving organic reactions and have collected 100+ transition structures with frequencies at several typical levels of theories. Such structures will be in upcoming Spartan 5.0 as TS building templates. Let me know if any specific TS-related question you have and I will gladly take a look at it. --Wayne -- +---------------------------------------------------------------+ | Wayne Huang, Ph.D. | 18401 Von Karman, Suite 370 | | Computational Chemist | Irvine, California 92612 | | Wavefunction, Inc. | 714-955-2120 <> 955-2118(fax)| | huang@wavefun.com | Web: http://www.wavefun.com | +---------------------------------------------------------------+ From fredhag@purdue.edu Wed May 21 23:43:54 1997 Received: from herald.cc.purdue.edu for fredhag@purdue.edu by www.ccl.net (8.8.3/950822.1) id XAA09748; Wed, 21 May 1997 23:03:46 -0400 (EDT) Received: from helios.cc.purdue.edu by herald.cc.purdue.edu; Wed, 21 May 97 22:03:45 -0500 Message-ID: <3383B791.39A680BA@purdue.edu> Date: Wed, 21 May 1997 22:03:45 -0500 From: "Fredrick C. Hagemeister" Organization: Purdue University Chemistry Department X-Mailer: Mozilla 4.0b4 [en] (Win95; I) MIME-Version: 1.0 To: Jaime Martell CC: Chia-Ning Yang , chemistry@www.ccl.net Subject: Re: CCL:G:Conv=N command in G94 X-Priority: 3 (Normal) References: Content-Type: text/plain; charset=iso-8859-1 Jaime Martell wrote: > On Wed, 21 May 1997, Chia-Ning Yang wrote: > > > Hello, > > I happen to forget where to put the command Conver=N in > > g94 input file. Can somebody answer me this? > > Thanks. > > C. Yang > > > > Wherever the G94 manual tells you to put it. My apology if you don't > have > a manual, but doesn't Gaussian still supply them with every purchase? > It > just seems to me that a large portion of the questions asked here > could > better be answered by searching in manuals, or calling or e-mailing > the > appropriate help desk (Gaussian or whomever is your favourite software > > vendor). > > Jaime Martell, Ph.D. Phone: (519) 824-4120 Ext. > 8520 > Department of Chemistry & Biochemistry E-mail: jmartell@uoguelph.ca > University of Guelph > Guelph, Ontario, Canada N1G 2W1 I think I understand both sides. On one hand, yes, I believe that people should first try to find an answer through traditional methods (manuals/docs and tech. support). Especially, when bandwidth is at stake! :-) However, some legitimate Gaussian users may not have documentation available. Those people using a network/mainframe version and others who have G9x access through such grants as NCSA SAP's, do not have the same access that others with a copy on their desks have. Further, I recently had a similar problem in which a CCL contributor suggested to another to use the "extended frequency output keyword" to get the G92 style normal modes in Cartesian coordinates. Of course, I knew I was in trouble when the phrase was in plain English (since such instances never result in the actual command parameter syntax !). I looked through my G94 manual (located within a foot of me) to find no such keyword. I tried using P in the router which, of course, only gave me some extra polarizability info. and a frequency stick plot. One line in the manual hinted at going to the companion text, and of course, I hadn't purchased it. I was finally successful when I went to Gaussian's fairly new web site and found it. BTW, it is FREQ=HPMODES. I suggest to Chia-Ning Yang to check out www.gaussian.com. It has a more complete version of the docs than the manual they send out! To Jaime Martell, I suggest when you see a message with a subject heading like "CCL:G:Conv=N command in G94," expect to find someone needing to know about the Conv=N command in G94 rather than someone giving some potentially important information about Conv=N. Hence, you can _skip_ that message and save yourself the time. -- *************************************************** * Fredrick (Fred) C. Hagemeister * * Dept. of Chemistry - Div. of Physical Chemistry * * Purdue University * * 1393 Brown Bldg * * West Lafayette, IN 47907-1393 * * ph.(317)494-7792 home/ans.machn.(317)474-2303 * * fredhag@purdue.edu * ***************************************************