From zhy@pchsgi25.IPC.PKU.EDU.CN Thu Apr 20 02:32:14 1995 Received: from pchsgi25.IPC.PKU.EDU.CN for zhy@pchsgi25.IPC.PKU.EDU.CN by www.ccl.net (8.6.10/930601.1506) id CAA08367; Thu, 20 Apr 1995 02:21:19 -0400 Received: by pchsgi25.IPC.PKU.EDU.CN (911016.SGI/911001.SGI) for chemistry@ccl.net id AA04573; Mon, 20 Mar 95 06:21:19 GMT Date: Mon, 20 Mar 1995 14:21:18 +0800 (SST) From: Zhang Hongyu To: COMP_CHEM_LIST Subject: Summary of "How to link atoms in SYBYL?" Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, everyone, Thanks for your helpful advices to my query on atom connection in sybyl. Here is a summary. My original question is > > Dear netters, > > Here is a question about SYBYL. > > When I use SYBYL to read a molecular coordinate file, such as PDB > file, sometimes many peptide atoms were discret in the screen, without > bond linked to each other. I know there is a menu in QUANTA able to link > them together with algorithms such as distance search. I wonder if there > is any similar function in SYBYL. > Thanks for your helpful advices. > > Henry H. Zhang > =================================================================== From: "Robert F. Setlik" Check to see if you are using the correct dictionary. I know that if, for example, you bring in a DNA PDB file while in the PROTEIN dictionary, the residues will not be connected. Also if the distance between the atoms of the peptide bond are abnormally distant, SYBYL may not put in the bond. However if you are bringing in a protein PDB with the PROTEIN dictionary, which is the default, the individual amino acids will be connected automatically. Hope this helps!! Rob Setlik _______________________________________________________________ Robert F. Setlik Biophysics Department, Roswell Park Cancer Institute, Buffalo, NY 14263 CCC 218 Phone (716) 845-3048 (Lab) Fax: (716) 845-8906 Email: setlik@acsu.buffalo.edu Member of the 'Buffalo Bill's four time Superbowl loss support and crisis group'. _______________________________________________________________ =============================================================== From: Emil Marcus When you bring in the PDB file, do not CENTER ! Than use the CRYSIN functionality. Emil Emil Marcus Department of Biophysics University at Buffalo marcus@acsu.buffalo.edu =============================================================== From: blakejf@giris4.pfizer.com (James F. Blake) Henry, I wrote a simple SPL script to do what you want. Save the below script as "fixbonds.spl" and then type "take fixbonds.spl" at the "Sybyl>" prompt. After you read a molecule in, you can type the command "fixbonds m1" for a molecule in molecular area m1 and it will connect the bonds. Jim Blake (blakejf@pfizer.com) ( ! I am sorry to omit the original code FOR COPYRIGHT REASON, if anyone want the code, please directly contact with Mr. Jim Blake ) ===================================================================== From: E.E.Moret The QUANTA comparable distance connectivity search can be found under BUILD/EDIT CRYSTALS in menumode or CRYSIN CONNECT in command mode. Regards Ed Moret ------------------------------------------------------------------------- E.E. Moret (@more@) E.E.Moret@far.ruu.nl Computational Medicinal Chemistry/Department of Pharmaceutical Chemistry Faculty of Pharmacy/Utrecht University/the Netherlands Telephone (31-30)536979/536958 Facsimile (31-30)516674 ------------------------------------------------------------------------- ===================================================================== From: jaeger@3dp.com (Ed Jaeger) Henry, I believe that there is a tailor setting for the Brookhaven which allows one to adjust the distance criteria used to identifying adjacent residues. Just look under 'tailor set brookhaven' for some leads. Ed Jaeger 3-Dimensional Pharmaceuticals, Inc. ph:610-458-6052 jaeger@3dp.com 665 Stockton Drive, Suite 104, Exton, PA 19341 fx:610-458-8249 From JOUBERT@physnet.phys.wits.ac.za Thu Apr 20 07:01:36 1995 Received: from caesar for JOUBERT@physnet.phys.wits.ac.za by www.ccl.net (8.6.10/930601.1506) id GAA10348; Thu, 20 Apr 1995 06:55:06 -0400 Received: from physnet.phys.wits.ac.za ([146.141.74.41]) by caesar (5.0/SMI-SVR4) id AA03417; Thu, 20 Apr 1995 12:49:03 +0200 Received: from PHYSNET/SpoolDir by physnet.phys.wits.ac.za (Mercury 1.12); Thu, 20 Apr 95 12:57:18 GMT +2:00 Received: from SpoolDir by PHYSNET (Mercury 1.12); Thu, 20 Apr 95 12:57:03 GMT +2:00 From: "Daniel " Organization: Wits University Physics Dept. To: chemistry@ccl.net Date: Thu, 20 Apr 1995 12:56:56 GMT + 2:00 Subject: CI code X-Pmrqc: 1 Return-Receipt-To: "Daniel " Priority: normal X-Mailer: Pegasus Mail/Windows (v1.11a) Message-Id: <4C8B7670A@physnet.phys.wits.ac.za> content-length: 535 Dear Netters I would appreciate any information on where I could obtain code to perform Configuration Interaction Calculations on atoms. Thank you Daniel Joubert ********************************************************************** Daniel Joubert Department of Physics University of the Witwatersrand P O Wits 2050 Johannesburg South Africa Phone: 27-11-7162059 (international) Fax: 27-11-3398262 (international) e-mail: joubert@physnet.phys.wits.ac.za ********************************************************************** From friedman@tammy.harvard.edu Thu Apr 20 09:31:39 1995 Received: from tammy.harvard.edu for friedman@tammy.harvard.edu by www.ccl.net (8.6.10/930601.1506) id JAA11931; Thu, 20 Apr 1995 09:21:44 -0400 Received: by tammy.harvard.edu (5.64/10.0) id AA22923; Thu, 20 Apr 95 09:24:35 -0400 Date: Thu, 20 Apr 95 09:24:35 -0400 From: friedman@tammy.harvard.edu (Dawn Friedman) Message-Id: <9504201324.AA22923@tammy.harvard.edu> To: chemistry@ccl.net, mfrancl@cc.brynmawr.edu Subject: Re: CCL:bug in G92 calculation of corrections for enthalpies Cc: friedman@tammy.harvard.edu Hi! How are you doing? I'm just finishing up a thesis chapter on the gauche effect, which has been haunting me since 1981, one way or another. What have you been up to? I hope all is well. Thanks, by the way, for redeeming that paper on anionic hyperconjugation. --Dawn Friedman (P'ton '83, LCA) From theochem@ctc.com Thu Apr 20 10:01:39 1995 Received: from server1.ctc.com for theochem@ctc.com by www.ccl.net (8.6.10/930601.1506) id JAA12480; Thu, 20 Apr 1995 09:59:45 -0400 Received: by server1.ctc.com (5.65/DEC-Ultrix/4.3) id AA16612; Thu, 20 Apr 1995 09:59:46 -0400 Received: by pauling.ctc.com (931110.SGI/930416.SGI.AUTO) for @server1.ctc.com:chemistry@ccl.net id AA10774; Thu, 20 Apr 95 10:56:59 -0400 From: theochem@ctc.com (Douglas Smith) Message-Id: <9504201456.AA10774@pauling.ctc.com> Subject: reference to COSMO To: chemistry@ccl.net (Computational Chemistry List) Date: Thu, 20 Apr 1995 10:56:56 -0500 (EDT) X-Mailer: ELM [version 2.4 PL22] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 564 Would someone pleae provide me with the reference(s) for the COSMO solvation method included in MOPAC 93? Does anyone have a brief description of the method? Doug -- Douglas A. Smith Principal Technical Staff/Theoretical Chemist Concurrent Technologies Corporation 1450 Scalp Avenue Johnstown, PA 15904 voice: (814) 269-2545 fax: (814) 269-2798 email: theochem@ctc.com Stadnard Disclamur: All opinions, comments, mistakes, endorsements and odd noises are my own, not my employer's. I would rather be and optimist and wrong than a pessimist and right. From mfrancl@cc.brynmawr.edu Thu Apr 20 10:16:38 1995 Received: from cc.brynmawr.edu for mfrancl@cc.brynmawr.edu by www.ccl.net (8.6.10/930601.1506) id KAA12959; Thu, 20 Apr 1995 10:10:24 -0400 Received: by cc.brynmawr.edu (5.65/DEC-Ultrix/4.4) id AA03110; Thu, 20 Apr 1995 10:11:24 -0400 Message-Id: <9504201411.AA03110@cc.brynmawr.edu> Subject: Re: CCL:G92 calculation of corrections for enthalpies To: chemistry@ccl.net Date: Thu, 20 Apr 95 10:11:24 EDT From: Francl Michelle M In-Reply-To: ; from "Michael Frisch" at Apr 19, 95 5:47 pm X-Mailer: ELM [version 2.3 PL11] In response to Mike Frisch and to further clarify my earlier post: As noted in my second post to CCL, I figured out that the thermal energies included the zero point energy. The point isn't terribly clear from the documentation. Thermal energy isn't a term that McQuarrie uses either, so again it's unclear exactly what is being done. Since ZPE is not a function of temperature, again I wouldn't have imagined it was included in something called "thermal energies". Michelle M. Francl Associate Professor of Chemistry Bryn Mawr College mfrancl@cc.brynmawr.edu From h0159cap@rz.hu-berlin.de Thu Apr 20 10:46:39 1995 Received: from hpcom.rz.hu-berlin.de for h0159cap@rz.hu-berlin.de by www.ccl.net (8.6.10/930601.1506) id KAA13587; Thu, 20 Apr 1995 10:30:20 -0400 Received: from ejoker.rz.hu-berlin.de by hpcom.rz.hu-berlin.de with SMTP (1.38.193.5/15.6-10.92) id AA04660; Thu, 20 Apr 1995 16:28:59 +0200 Received: from localhost by joker.rz.hu-berlin.de (8.6.4/X1.00.syb) id QAA08458; Thu, 20 Apr 1995 16:28:37 +0200 From: h0159cap@rz.hu-berlin.de (Frank Eisenmenger) Message-Id: <199504201428.QAA08458@joker.rz.hu-berlin.de> Subject: autocorrelation for dihedrals To: CHEMISTRY@ccl.net Date: Thu, 20 Apr 1995 16:28:37 +0200 (MET) X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 2730 Dear CCL-ers, recently, I posted the following question: > during conformational analysis of peptides the following question occurred: > given a (time-)series of conformations of a linear four-atom molecule > described by one dihedral angle (=tau, range 180 ... +180) > > How calculate the autocorrelation function for tau, taking into account the > "cyclic" behaviour of dihedrals ? A number of replies and our own efforts helped to produce the following routine, which can serve as a first step in solving the above problem: -------------------------------------------------------------------------- real*4 function avrang(n,angs,idx) c ------------------------------------------ c PURPOSE: average of N angles given in c array ANGS ( all from [-pi,pi] ) c c ! array IDX must provide ASCENDING c order for angles (1...n) on INPUT c c 0 < EPS < 1 ensures that angles c EVENLY & DENSLY distributed in [-pi,pi] c have average close to 0.0 c c K. Peters & F. Eisenmenger April 1995 c Inst. of Biochemistry c Med. Faculty of Humboldt Univ. Berlin c ------------------------------------------ implicit real*4 (a-h,o-z) implicit integer (i-n) c parameter (pi=3.141592653589793, c # pi2=2.0*pi) parameter (pi=180.0, # pi2=2.0*pi) parameter (eps=0.95) dimension angs(*),idx(*) ai=angs(idx(1)) dm=angs(idx(n))-ai im=1 av=ai ap=ai+pi2 do i=2,n ai=angs(idx(i)) d=ap-ai if (d.lt.eps*dm) then dm=d im=i endif av=av+ai ap=ai+pi2 enddo av=(av+float(im-1)*pi2)/float(n) if (abs(av).gt.pi) av=av-sign(pi2,av) avrang=av return end -------------------------------------------------------------------------- Feel free to test/apply this. I would be happy about any suggestions. Good luck, Frank Eisenmenger +------------------------------------------------------------------------+ | Institute of Biochemistry | | Medical Faculty of the Humboldt University (Charite) | | | | Hessische Str. 3-4 | | 10115 Berlin, Germany | | | | Phone: +49-30-28468-612 or -239 FAX: +49-30-28468-600 | | E-mail: h0159cap@joker.rz.hu-berlin.de | +------------------------------------------------------------------------+ From C1790@SLVAXA.UMSL.EDU Thu Apr 20 12:16:41 1995 Received: from SLVAXA for C1790@SLVAXA.UMSL.EDU by www.ccl.net (8.6.10/930601.1506) id MAA15435; Thu, 20 Apr 1995 12:04:32 -0400 Received: from SLVAXA.UMSL.EDU by SLVAXA.UMSL.EDU (PMDF V4.3-7 #2503) id <01HPK5R9TOY4BQ0UPW@SLVAXA.UMSL.EDU>; Thu, 20 Apr 1995 11:05:36 CDT Date: Thu, 20 Apr 1995 11:05:36 -0500 (CDT) From: BILL WELSH Subject: Contacts for Macromodel To: Chemistry@ccl.net Message-id: <01HPK5R9TOY6BQ0UPW@SLVAXA.UMSL.EDU> X-VMS-To: IN%"Chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Our System Manager needs to contact people at Macromodel who might answer a few questions about its portability to other systems. He tells me that he is having trouble getting responses when he uses the email address and phone number for Macromodel that I gave him. Can someone give me a sure-fire email address and/or phone number at Macromodel (Columbia U.) for my colleague? Thanks ... Bill Welsh Univ. of Missouri-St. Louis c1790@slvaxa.umsl.edu From shenkin@still3.chem.columbia.edu Thu Apr 20 13:46:41 1995 Received: from mailhub.cc.columbia.edu for shenkin@still3.chem.columbia.edu by www.ccl.net (8.6.10/930601.1506) id NAA17699; Thu, 20 Apr 1995 13:39:51 -0400 Received: from still3.chem.columbia.edu by mailhub.cc.columbia.edu with SMTP id AA12395 (5.65c+CU/IDA-1.4.4/HLK for <@mailhub.cc.columbia.edu:Chemistry@ccl.net>); Thu, 20 Apr 1995 13:39:50 -0400 Received: by still3.chem.columbia.edu (931110.SGI/930416.SGI.AUTO) for @mailhub.cc.columbia.edu:Chemistry@ccl.net id AA02708; Thu, 20 Apr 95 13:39:49 -0400 From: "Peter Shenkin" Message-Id: <9504201339.ZM2706@still3.chem.columbia.edu> Date: Thu, 20 Apr 1995 13:39:46 -0400 In-Reply-To: BILL WELSH "CCL:Contacts for Macromodel" (Apr 20, 11:05am) References: <01HPK5R9TOY6BQ0UPW@SLVAXA.UMSL.EDU> X-Mailer: Z-Mail (3.1.0 22feb94 MediaMail) To: BILL WELSH , Chemistry@ccl.net Subject: Re: CCL:Contacts for Macromodel Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 On Apr 20, 11:05am, BILL WELSH wrote: > Subject: CCL:Contacts for Macromodel > Our System Manager needs to contact people at Macromodel who might answer > a few questions about its portability to other systems. He tells me that he > is having trouble getting responses when he uses the email address and > phone number for Macromodel that I gave him. Email: mmod@still3.chem.columbia.edu Voice: (212) 854-8402 FAX: (212) 678-9039 -P. -- ************************ The secret of life: ************************* *Peter S. Shenkin, Box 768 Havemeyer Hall, Chemistry, Columbia Univ.,* * New York, NY 10027; shenkin@columbia.edu; (212) 854-5143 * ************* If you find a loose thread, don't pull it. ************* From fer@bilbo.edu.uy Thu Apr 20 14:01:42 1995 Received: from seciu.uy for fer@bilbo.edu.uy by www.ccl.net (8.6.10/930601.1506) id NAA18038; Thu, 20 Apr 1995 13:52:10 -0400 Received: from bilbo.edu.uy by seciu.uy with smtp (Smail3.1.29.1 #1) id m0s20Kg-000m5mC; Thu, 20 Apr 95 14:48 GMT-3:00 Received: by bilbo.edu.uy (AIX 3.2/UCB 5.64/4.03) id AA19152; Thu, 20 Apr 1995 14:48:15 -0300 Date: Thu, 20 Apr 1995 14:48:15 -0300 (TZ ) From: Fernando Vila To: List CC Subject: How to draw Diagrams Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi!!, anybody knows where could be found a (small, user friendly) MS-Windows or DOS program to draw MBPT and Shavitt diagrams? Thanks in advance, Fernando. ******************************************************************************* Fernando Vila Catedra de Quimica Cuantica Tel. +(5982)941860 Facultad de Quimica Fax +(5982)941906 Gral.Flores 2124, C. C. 1157 E-mail fer@bilbo.edu.uy Montevideo 11800, URUGUAY WWW http://bilbo.edu.uy/MTC-Lab.html ******************************************************************************* From jpnort@mail.wm.edu Thu Apr 20 20:31:46 1995 Received: from mail.wm.edu for jpnort@mail.wm.edu by www.ccl.net (8.6.10/930601.1506) id UAA24650; Thu, 20 Apr 1995 20:16:44 -0400 Received: from gopher.cc.wm.edu by mail.wm.edu (AIX 3.2/UCB 5.64/4.03) id AA11152; Thu, 20 Apr 1995 20:07:17 -0400 Received: by gopher.cc.wm.edu (AIX 3.2/UCB 5.64/4.03) id AA30297; Thu, 20 Apr 1995 20:07:15 -0400 Date: Thu, 20 Apr 1995 20:07:14 -0400 (EDT) From: "J.P. Northrop" Subject: virus alert (fwd) To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I got this from a friend over the internet . . . PLEASE BE CAREFUL!!! ---------- Forwarded message ---------- Date: Thu, 20 Apr 1995 08:04:16 -0400 From: Sandra Obleas To: jpnort@mail.wm.edu Subject: virus alert Hi JP - Thought you might be interested in this e-mail I received from S3. SRO >Date: Tue, 18 Apr 1995 16:51:25 -0700 >From: barker@scubed.scubed.com (Terry Barker) >To: everyone@scubed.scubed.com >Subject: virus alert > >I'm forwarding this message to all from Matt Palmer..... >> >>The following virus alert was sent to me by Patti Charney, >>who received it from NOSC: >> >>NOSC >>Subject: "Virus Alert" >>Date: Thursday, 13 April, 1995 3:29PM >>Priority: High >> >>The following virus warning was provided to us by DOE: >> >>There is a computer virus that is being sent across the >>InterNet. If you receive an e-mail message with the subject >>line "Good Times", DO NOT read the message, DELETE >>it immediately. By reading the message, a virus is loaded >>into the mail server's ASCII buffer causing the "Good Times" >>program to initialize and execute. The program rewrites your >>hard drive, obliterating anything on it. If the program is not >>stopped, the computer's processor will be placed in an >>nth-complexity infinite binary loop - which can severely damage >>the processor. >> >>The program is highly intelligent - it will send >>copies of itself to everyone whose e-mail address is contained >>in a received-mail file or sent-mail file, if it can find one. It will >>then proceed to trash the computer it is running on. >> >>Warn your friends and local system users of this newest threat to the >>InterNet! It could save them a lot of time and money. >> >> >>M. Palmer >> >> >> > > >Terry Barker > > From hcj@mazda.wavefun.com Thu Apr 20 21:31:47 1995 Received: from volvo.wavefun.com for hcj@mazda.wavefun.com by www.ccl.net (8.6.10/930601.1506) id VAA25163; Thu, 20 Apr 1995 21:24:35 -0400 Received: by volvo.wavefun.com (931110.SGI/930416.SGI) for chemistry@ccl.net id AA13806; Thu, 20 Apr 95 18:24:54 -0700 Received: from mazda.wavefun.com(198.147.95.6) by volvo via smap (V1.3) id sma013804; Thu Apr 20 18:24:36 1995 Received: by mazda.wavefun.com (931110.SGI/930416.SGI) for @volvo.wavefun.com:chemistry@ccl.net id AA10794; Thu, 20 Apr 95 18:24:21 -0700 Date: Thu, 20 Apr 95 18:24:21 -0700 From: hcj@mazda.wavefun.com (Harry C. Johnson) Message-Id: <9504210124.AA10794@mazda.wavefun.com> To: jpnort@mail.wm.edu Cc: chemistry@ccl.net In-Reply-To: (jpnort@mail.wm.edu) Subject: Re: CCL:virus alert (fwd) Reply-To: hcj@wavefun.com >>> The following virus warning was provided to us by DOE: >>> >>> There is a computer virus that is being sent across the >>> InterNet. If you receive an e-mail message with the subject >>> line "Good Times", DO NOT read the message, DELETE it >>> immediately. By reading the message, a virus is loaded into >>> the mail server's ASCII buffer causing the "Good Times" >>> program to initialize and execute. The program rewrites your >>> hard drive, obliterating anything on it. If the program is >>> not stopped, the computer's processor will be placed in an >>> nth-complexity infinite binary loop - which can severely >>> damage the processor. >>> >>> The program is highly intelligent - it will send copies of >>> itself to everyone whose e-mail address is contained in a >>> received-mail file or sent-mail file, if it can find one. It >>> will then proceed to trash the computer it is running on. >>> >>> Warn your friends and local system users of this newest threat >>> to the InterNet! It could save them a lot of time and money. >>> This is a hoax. Recently on the firewalls mailing list this message has been discussed since it has re-emerged for apparently the second time. According to all of the responses from the security people on the list, e-mail is not a threat unless you foolishly save a message into a file and then execute that file without looking at it. -Harry +-----------------------+--------------------------------------------+ |Harry C. Johnson | /--- ----\ /---/ ---\ ----- /---/ /| / | |Computational Chemist | \ / / / / / / / / / / | / | |Wavefunction Inc. | \ /---/ /---/ /---/ / /---/ / | / | |E-mail: hcj@wavefun.com|---/ / / / / \ / / / / |/ | +-----------------------+--------------------------------------------+ From feng@london.ks.uiuc.edu Thu Apr 20 22:16:49 1995 Received: from london.ks.uiuc.edu for feng@london.ks.uiuc.edu by www.ccl.net (8.6.10/930601.1506) id WAA25615; Thu, 20 Apr 1995 22:10:06 -0400 Received: from leipzig.ks.uiuc.edu by london.ks.uiuc.edu with SMTP (1.37.109.16/16.2) id AA260270206; Thu, 20 Apr 1995 21:10:06 -0500 From: Zhou Feng Message-Id: <199504210210.AA260270206@london.ks.uiuc.edu> Received: by leipzig.ks.uiuc.edu (NX5.67d/NX3.0X) id AA22203; Thu, 20 Apr 95 21:10:05 -0500 Date: Thu, 20 Apr 95 21:10:05 -0500 Received: by NeXT.Mailer (1.100) Received: by NeXT Mailer (1.100) To: Chemistry@ccl.net Subject: solvation energy of phosphate in water Reply-To: feng@london.ks.uiuc.edu Dear all: I am looking for some experimental data of the solvation energy for phosphate groups (PO4-) group in water. Does any experimental value or theoretical value exist? Please send me a message if you can help. Thanks a lot! --- Feng Zhou +-------------------------------------------------------------------- |Theoretical Biophysics feng@lisboa.ks.uiuc.edu |University of Illinois Tel: (217)-244-5042 |3121 Beckman Institute Fax: (217)-244-6078 |405 N Mathews, Urbana, IL61801 NeXTmail Ok +--------------------------------------------------------------------