From mmh1203@ggr.co.uk Mon Feb 13 04:39:36 1995 Received: from gate.ggr.co.uk for mmh1203@ggr.co.uk by www.ccl.net (8.6.9/930601.1506) id EAA21254; Mon, 13 Feb 1995 04:33:31 -0500 Received: from mailhub.ggr.co.uk (uk0x07.ggr.co.uk) by gate.ggr.co.uk; Mon, 13 Feb 1995 09:31:07 GMT Received: from uk6x12.ggr.co.uk by mailhub.ggr.co.uk; Mon, 13 Feb 1995 09:23:11 GMT Received: by uk6x12.ggr.co.uk (8.6.8.1/imd110593) id JAA16752; Mon, 13 Feb 1995 09:31:59 GMT Date: Mon, 13 Feb 1995 09:31:57 +0000 (GMT) From: Mike Hann X-Sender: mmh1203@uk6x12 To: chemistry@ccl.net Subject: MGMS meeting and apology Message-ID: MIME-Version: 1.0 Content-Type: MULTIPART/MIXED; BOUNDARY="-1048570318-1989782578-792667917=:16739" This message is in MIME format. The first part should be readable text, while the remaining parts are likely unreadable without MIME-aware tools. Send mail to mime@docserver.cac.washington.edu for more info. ---1048570318-1989782578-792667917=:16739 Content-Type: TEXT/PLAIN; charset=US-ASCII My apologies for the "unreadable" message that I sent out last week about the MGMS meeting on Computational Chemistry aspects of CHemical Libraries. The corrected notice is attached. ---------------------------------------------------------------- Mike Hann Head of Computational Chemistry Glaxo Research and Development Greenford Rd Greenford Middlesex UB6 0HE England mmh1203@ggr.co.uk tel: 081-966-2413 fac: 081-966-2156 ---1048570318-1989782578-792667917=:16739 Content-Type: TEXT/PLAIN; charset=US-ASCII; name="leeds.lis" Content-Transfer-Encoding: BASE64 Content-ID: Content-Description: CQ0KCU1PTEVDVUxBUiBHUkFQSElDUyBBTkQgTU9ERUxMSU5HIFNPQ0lFVFkg KE1HTVMpDQoNCk1HTVMgTWVldGluZyAtIENPTVBVVEFUSU9OQUwgQVNQRUNU UyBPRiBDSEVNSUNBTCBMSUJSQVJJRVMNCiANCiANClRoZSB2ZW51ZSBmb3Ig dGhlIGFib3ZlIGNvbmZlcmVuY2UgaXMgRGV2b25zaGlyZSBIYWxsLCBVbml2 ZXJzaXR5IG9mIExlZWRzLCANCkxlZWRzLEVuZ2xhbmQgb24gdGhlIDEwLTEy IEFwcmlsIDE5OTUuDQogDQpUaGUgcHJvdmlzaW9uYWwgcHJvZ3JhbW1lIGlu Y2x1ZGVzIHRvcGljcyBvbiB0aGUgZm9sbG93aW5nOg0KIA0KMQlDYWxjdWxh dGluZyBjaGVtaWNhbCBkaXZlcnNpdHkgZm9yIHByb2ZpbGluZyBsaWJyYXJp ZXM7DQoyCURhdGEgc3RydWN0dXJlcyBhbmQgZGF0YWJhc2VzIGZvciBob2xk 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YXRpb24gcGxlYXNlIGNvbnRhY3QgR2lsbGlhbiBNYWNkb25hbGQgYXQgdGhl IGFib3ZlIA0KYWRkcmVzcywgdGVsZXBob25lIG51bWJlciArNDQgMTEzIDIz MyA2NTMwIG9yIGZheCArNDQgMTEzIDIzMyA2NTYzLg0KIA0KSWYgeW91IGFy ZSByZWdpc3RlcmluZyBieSBlbGVjdHJvbmljIG1haWwgeW91IHdpbGwgbm90 IGJlIA0Kb2ZmaWNpYWxseSByZWdpc3RlcmVkIHVudGlsIHlvdXIgY2hlcXVl IGhhcyBiZWVuIHJlY2VpdmVkLg0KIA0KX19fX19fX19fX19fX19fX19fX19f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fDQpUaGUg TUdNUyBpcyBhIHJlZ2lzdGVyZWQgY2hhcml0eSBpbiB0aGUgVUsNCg== ---1048570318-1989782578-792667917=:16739-- From emadtajk@IREARN.bitnet Mon Feb 13 08:39:34 1995 Received: from AWIUNI11.EDVZ.UniVie.AC.AT for emadtajk@IREARN.bitnet by www.ccl.net (8.6.9/930601.1506) id IAA23973; Mon, 13 Feb 1995 08:00:04 -0500 Received: from ROSE.IPM.AC.IR by AWIUNI11.EDVZ.UniVie.AC.AT (IBM VM SMTP V2R2) with TCP; Mon, 13 Feb 95 13:51:54 MEZ Received: by IREARN.BITNET (MX V4.1 VAX) id 1; Mon, 13 Feb 1995 16:20:47 +0330 Date: Mon, 13 Feb 1995 16:20:46 +0330 From: "E.TAJKHORSHID" To: chemistry@ccl.net CC: emadtajk@IREARN.bitnet Message-ID: <0098BEE6.390368E0.1@IREARN.BITNET> Subject: HELP on VAX SETUP Hello everybody, I am working on a vaxstation 3100, 16 mbyte memory, 76. I try to run AMBER 4.0 on this machine. But I get a DUMP MEMORY and HANG in my machine whenever I try to run the program. I think there is a problem in setting up my machine with appropriate parameters in system files. I will be so thankful if someone kindly send me a copy of the system files of his machine containing these parameters. Sincerely yours, Thanks in advance sincerely ******************************************************************************** Emadeddin Tajkhorshid EMADTAJK@irearn.bitnet Dept. Medicinal Chemistry, School of Pharmacy, TEL: 98 21 6112928 Tehran Univ. Medical Sciences, FAX: 98 21 6461178 P. O. Box 14155/6451, TEHRAN, IRAN ******************************************************************************* From emadtajk@IREARN.bitnet Mon Feb 13 08:49:17 1995 Received: from AWIUNI11.EDVZ.UniVie.AC.AT for emadtajk@IREARN.bitnet by www.ccl.net (8.6.9/930601.1506) id IAA23984; Mon, 13 Feb 1995 08:00:24 -0500 Received: from ROSE.IPM.AC.IR by AWIUNI11.EDVZ.UniVie.AC.AT (IBM VM SMTP V2R2) with TCP; Mon, 13 Feb 95 13:52:48 MEZ Received: by IREARN.BITNET (MX V4.1 VAX) id 170; Mon, 13 Feb 1995 16:21:09 +0330 Date: Mon, 13 Feb 1995 16:21:08 +0330 From: "E.TAJKHORSHID" To: chemistry@ccl.net CC: emadtajk@IREARN.bitnet Message-ID: <0098BEE6.4604E0A0.170@IREARN.BITNET> Subject: CONGRES ANNOUNCEMENT >> 12th IRANIAN CONGRESS OF PHYSIOLOGY AND PHARMACOLOGY << Organized by the Iran University of Medical Sciences in Collaboration with Iranian Society of Physiology and Pharmacology Tehran (Iran), November 6-9, 1995 ****************************************************************************** Dear Colleague: The organizing committee of the 12th ICPP is honored to invite you to participate actively in this meeting. ****************************************************************************** TOPICS (Code): 1) Adverse Drug Reactions (100) 2) Aging (Gerontology) (101) 3) Autonomic Nervous System (102) 4) Biochemistry (103) 5) Biophysics and Biomedical Engineering (104) 6) Biopharmaceutics and Pharmacokinetics (105) 7) Blood and Blood Components (106) 8) Cancer and Neoplasia (107) 9) Cellular and General Physiology (108) 10) Central Nervous Systenm (109) 11) Chemotherapeutic Agents (110) 12) Clinical Pharmacology and Therapeutics (111) 13) Comparative Physiology (112) 14) Developmental Pharmacology and Toxicology (113) 15) Drug Interaction (114) 16) Endocrine System and Reproduction (115) 17) Environmental and Exercise Physiology (116) 18) Enzymes and Enzyme Regulation (117) 19) Ethnopharmacology (118) 20) Gastrointestinal Pharmacology (119) 21) Genetics (120) 22) Heart and Circulation (121) 23) Immunology and Immunopharmacology (122) 24) Inflamnmation and Anti-Inflammatory Agents (123) 25) Local Hormones and Autocoides (124) 26) Membrane and Transport (125) 27) Nutrition (126) 28) Pathobiology (127) 29) Pharmaceutical Chemistry (128) 30) Pharmacognosy (129) 31) Receptor and Molecular Pharmacology (130) 32) Renal Physiology and Pharmacology (131) 33) Respiratory System (132) 34) Toxicology (133) 35) Veterinary Physiology and Pharmacology (134) ****************************************************************************** Free communications will be presented solely as poster presentation. Abstract deadline: MAY 31, 1995 Deadline for abstract submission: April 30, 1995 Language: English / Farsi ------------------------------------------------------------------------------ Registration Form Title: Prof/Dr/Mr/Mrs/Miss/Ms Complete Name: Sex: Degree: Institutional Affiliation: Position Held: Mailing Address: Presenting: Poster ( ) Seminar ( ) Workshop ( ) None ( ) Category Code as appeared in the topic list: 1st. Choice [ ] 2nd Choice [ ] Registration Fees: Prior to June 31, 95 300 US$ ( ) After June 31, 95 400 US$ ( ) Student* 150 US$ ( ) * Please enclose proof of your student status. Payments: Please draft the registration fee, payable to: Prof. Massoud Mahmoudian, Secretary of 12th ICPP, in Bank Melli Iran, Eskan branch, Code 271, Tehran,IRAN and mail the receipt with the registration form to the congress secretary. ------------------------------------------------------------------------------ Just for visa applicants: Father's name: Date and place of birth: Nationality: Occupation: Passport No.: Date & place of issue: Exp. date: Place where visa to be issued: Duration of staying in IRAN: ////////////////////////////////////////////////////////////////////////////// ------------------------------------------------------------------------------ You may fill and email the registration form (and your abstract) to: MASMAH73@IREARN.BITNET ------------------------------------------------------------------------------ For further information contact: Prof. M. Mahmoudian Secretary of the Congress, International Relations Dept., Iran Universioty of Medical Sciences, P.O.Box 15875/6171, Tehran, IRAN FAX: +98-21-8016207 E-MAIL: MASMAH73@IREARN.BITNET From Bernd.Hartke@RUS.Uni-Stuttgart.DE Mon Feb 13 09:39:28 1995 Received: from dfunms.rus.uni-stuttgart.de for Bernd.Hartke@RUS.Uni-Stuttgart.DE by www.ccl.net (8.6.9/930601.1506) id IAA24554; Mon, 13 Feb 1995 08:47:56 -0500 From: Received: from servus02.rus.uni-stuttgart.de by dfunms.rus.uni-stuttgart.de with SMTP id AA15240 (5.65c8/DFUE-M1.0 for ); Mon, 13 Feb 1995 14:29:25 +0100 Received: from servus07.rus.uni-stuttgart.de by servus02.rus.uni-stuttgart.de (AIX 3.2/UCB 5.64/SERVus-1.2) id AA34408; Mon, 13 Feb 1995 14:29:24 +0100 Received: by servus07.rus.uni-stuttgart.de (AIX 3.2/UCB 5.64/4.03) id AA32662; Mon, 13 Feb 1995 14:29:23 +0100 Message-Id: <9502131329.AA32662@servus07.rus.uni-stuttgart.de> Subject: CCL: summary: distance geometry programs To: CHEMISTRY@ccl.net Date: Mon, 13 Feb 1995 14:29:22 +0100 (MEZ) Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 4622 Dear netters, last week I inquired about distance geometry programs, and I received several replies. I have attached them below in a slightly shortened form. Some of the respondents informed me that the QCPE abstract for the program #590 "DGEOM" is out of date, with respect to the form in which it is shipped. I asked QCPE about this, and they told me that the new 1995 version of DGEOM will soon be available (advance orders are being accepted already), it will be completely unix, and it will be delivered in virtually any form (including ftp delivery or pickup). Thank you very much for your help! Bernd -- Dr. Bernd Hartke e-mail: bernd.hartke@rus.uni-stuttgart.de Dep. of Theoretical Chemistry e-mail: bxh@wiffin.chem.ucla.edu University of Stuttgart Pfaffenwaldring 55 Phone: +49-711-685-4409 70569 Stuttgart FAX: +49-711-685-4442 GERMANY ================ list of replies: --------------------------------------------------------------------- From: thep@risc1.lrm.fi.cnr.it (Pornthep Sompornpisut) The program DIANA (Distance Geometry Algorithm for NMR Applications) operates in torsion angle space, performing a least-squares minimization of variable target function through manipulation of single, rotatable bonds in a generated sequence of amino acids. Diatance and dihedral angle constraints are used to calculate protein structures. The program is written in standard FORTRAN-77 and also available for Unix. However I think it's a commercial program. For further information, you can cantact Peter Guntert guentert@molbio.ethz.ch Hope this help Pornthep --------------------------------------------------------------------- From: rull@rhino.chem.ruu.nl (Ton Rullmann) I suspect that the DG program package developed by dr. Ruud Scheek from the University of Groningen might be useful. We have been using it extensively in the past. It is in Fortran, has separate modules for setup, embedding, smoothbounding etc, and the modules interact via bounds and distance matrices written to disk. I don't know anything about the current state of the program, but you might contact the author: Dr. Ruud M. Scheek Department of Biophysical Chemistry University of Groningen Nijenborgh 4 9747 AG Groningen The Netherlands Phone: +31 50 634328 Fax: +31 50 634800 Email: scheek@chem.rug.nl Good luck! Ton Rullmann. --------------------------------------------------------------------- From: wells@athens.dental.upenn.edu (Gregg B. Wells) Bernd, the description of DGEOM fromthe QCPE is out of date. The program is available in several other formats besides BACKUP. You can ask the QCPE about the availability of DGEOM for whatever platfor you want to use. Gregg Wells --------------------------------------------------------------------- From: xiao@bohr.mssm.edu (Dr. Leon Xiao) There are several places you may get the DG program for your purpose. 1. QCPE590 in Fortran, which you have already had. 2. DG-II, a commercial package comes with InsightII/NMR module by Biosym, can read in just distance constraint matrix. 3. From Prof. Tom Hayden, University of Kentucky, USA. His program may best serve your purpose. It is in C and I was helping him to develop it. I think you can get it free. You can send E-mail to hayden@ms.uky.edu or write to Prof. Tom Hayden University of Kentucky Mathematical Sciences 715 Patterson Office Tower Lexington, Kentucky 40506-0027 Good luck ! Leon Y. Xiao --------------------------------------------------------------------- From: WallyR@netcom.netcom.com (Walter E. Reiher III) The copy I bought from QCPE last fall came on a 1/4 in cartridge tape in UNIX tar format. Also, it's in FORTRAN. QCPE will deliver to you via FTP, if you prefer. I don't understand your complaint about PDB format--it's simply a common way of expressing a molecule's connection table and 3D coordinates. If anything, I find DGEOM much less protein-specific than many other programs out there. Wally --------------------------------------------------------------------- From: dixons%phvax.dnet@sb.com The DGEOM program is not all that tied to chemistry. PDB format is easy to generate or it is possible to input a bounds matrix directly and also get back out a bounds matrix if you wish. The program runs fine on Unix boxes and I am sure that you can get it in other than VAX backup format if you wish. You will need to license it from QCPE first and then if they cannot supply it in a suitable format, let me know and I will help out. Regards, Scott Dixon From mmh1203@ggr.co.uk Mon Feb 13 09:45:11 1995 Received: from gate.ggr.co.uk for mmh1203@ggr.co.uk by www.ccl.net (8.6.9/930601.1506) id IAA24691; Mon, 13 Feb 1995 08:52:25 -0500 Received: from mailhub.ggr.co.uk (uk0x07.ggr.co.uk) by gate.ggr.co.uk; Mon, 13 Feb 1995 13:50:04 GMT Message-Id: <4287.199502131342@mailhub.ggr.co.uk> Received: from UKSYSA.ggr.co.uk by mailhub.ggr.co.uk; Mon, 13 Feb 1995 13:42:04 GMT From: Dr M M Hann Date: 13 Feb 95 13:39:00 GMT Subject: MGMS meeting in Leeds - Computers and Combinatorial Chemistry To: chemistry@ccl.net It would appear that the CCL mailer is continuing to strip the MIME header of my file so I have returned to the VAX mail system. My apologies once again for filling up disk space and wasting your valuable reading time. Mike Hann -------------------------------- ATTACHMENT -------------------------------- Created: 13-Feb-1995 01:36pm Posted : 13-Feb-1995 12:00am >From : @ Subject: MGMS meeting in Leeds MOLECULAR GRAPHICS AND MODELLING SOCIETY (MGMS) MGMS Meeting - COMPUTATIONAL ASPECTS OF CHEMICAL LIBRARIES The venue for the above conference is Devonshire Hall, University of Leeds, Leeds,England on the 10-12 April 1995. The provisional programme includes topics on the following: 1 Calculating chemical diversity for profiling libraries; 2 Data structures and databases for holding library information; 3 Computational analysis and data mining; 4 Searching of reaction databases and other computational aids to wet chemistry. The following is a list of speakers who have already accepted: Eric Gordon (Affymax) Jim Dunbar (Parke Davis) Yvonne Martin (Abbott) Ed Maliski (Glaxo Inc) David Spellmeyer (Chiron) Jeff Morris (Zeneca) John Bradshaw/Darko Butina (Glaxo) Dick Cramer (Tripos) Bernie Rhode (Ciba) Paul Finn (Pfizer) Keith Davis (CDL) Speakers from MDL and Daylight are also expected. In addition to these and other invited speakers, additional oral and poster contributions are welcomed. Please send title and abstract of the proposed contribution by February 28, 1995. The organisers will notify applicants by 13th March whether their work can be presented through an oral presentation or a poster. There are also a limited number of student bursaries available. These will be allocated by the 1st March. One criterion will be the presentation of a piece of work either orally or as a poster. The amount awarded will depend on circumstances, however, the Molecular Graphics and Modelling Society committee is particularly anxious that young research workers in this field have the opportunity to attend. In addition, there will be a #50 prize for the best poster presented by a student. The meeting includes a software/hardware exhibition. Please contact the organisers for details. Closing date for registrations is 20th March 1995. The meeting is limited to 120 participants in total and there is considerable interest, so register early! This announcement also serves as notice of the 1995 Annual General Meeting of the Molecular Graphics and Modelling Society to be held on 10 April 1995, at 6.30 p.m. Any motions for this meeting should be sent to Dr Mike A King, MGMS Secretary, Shell Research bv, Koninklijke/Shell-Laboratorium Amsterdam, PO Box 38000, 1030 BN Amsterdam, Netherlands, Tel +31 20 630 2444, Fax +31 20 630 4037, email king1@ksla.nl by 11th March 1995. Registration details are as follows (costs are pound sterling): Accommodation is at Devonshire Hall. Overnight accommodation #23.50 per night (Bed and breakfast) Lunch #8.00 per day Dinner #11.00 per day (except on Tuesday - Banquet #25.00) R E G I S T R A T I O N F O R M Registration: (Before 20th March 1995) Student #50 ............. Full member #90 ............. Non member #120 .............. (After 20th March 1995) Student #70 ............. Full member #110 ............. Non member #140 ............. Sunday, 9 April Dinner 11.00 .......... Accommodation 23.50 .......... Monday, 10 April Lunch 8.00 .......... Dinner 11.00 .......... Accommodation 23.50 .......... Tuesday, 11 April Lunch 8.00 .......... Banquet 25.00 .......... Accommodation 23.50 .......... Wednesday, 12 April Lunch 8.00 .......... Dinner 11.00 ........... Accommodation 23.50 .......... Please advise of dietary or other special requirements. I wish to present a poster (Yes/No) I would be prepared to give an oral presentation (Yes/No) (Note that for both the above a title and brief abstract must reach Leeds by 15 February 1995 Please return this form and a cheque for the correct amount in pounds sterling, made payable to the University of Leeds; to Dr A P Johnson, ICAMS, School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK. If you require any further information please contact Gillian Macdonald at the above address, telephone number +44 113 233 6530 or fax +44 113 233 6563. If you are registering by electronic mail you will not be officially registered until your cheque has been received. ____________________________________________________________ The MGMS is a registered charity in the UK From unipune.ernet.in!gadre@unipune.ernet.in Mon Feb 13 10:39:31 1995 Received: from sangam.ncst.ernet.in for unipune.ernet.in!gadre@unipune.ernet.in by www.ccl.net (8.6.9/930601.1506) id JAA25934; Mon, 13 Feb 1995 09:49:13 -0500 Received: from unipune.UUCP (root@localhost) by sangam.ncst.ernet.in (8.6.8.1/8.6.6) with UUCP id UAA05293 for CHEMISTRY@ccl.net; Mon, 13 Feb 1995 20:18:42 +0530 Received: from unipune.UUCP by iucaa (4.1/SMI-4.1) id AA05907; Mon, 13 Feb 95 17:46:05+050 Received: by unipune.unipune.ernet.in (5.0/SMI-SVR4) id AA11158; Mon, 13 Feb 1995 17:22:50 +0500 Date: Mon, 13 Feb 1995 17:22:50 +0500 From: gadre@unipune.ernet.in (Faculty) Message-Id: <9502132222.AA11158@unipune.unipune.ernet.in> To: CHEMISTRY@ccl.net Subject: GRAPHICS on 80486 with svga color monitor Content-Length: 328 ATTRACTIVE 2D/3D Graphics is available with van der walls with and without texture, planar cross sections with transparency, isosurfaces and many more facilities. If interested, contact : gadre@unipune.ernet.in OR gadre@parcom.ernet.in FAX : 0091-212-337551 OR 333899. This is a unique visualization package. Don't miss it! From Karl.F.Moschner@urlus.sprint.com Mon Feb 13 10:41:15 1995 Received: from sprintf.merit.edu for Karl.F.Moschner@urlus.sprint.com by www.ccl.net (8.6.9/930601.1506) id KAA26208; Mon, 13 Feb 1995 10:03:47 -0500 X400-Received: by mta merit in /PRMD=internet/ADMD=telemail/C=us/; Relayed; Mon, 13 Feb 1995 09:54:07 -0500 X400-Received: by /ADMD=TELEMAIL/C=US/; Relayed; Mon, 13 Feb 1995 09:39:56 -0500 X400-Received: by /PRMD=SMXFL2/ADMD=TELEMAIL/C=US/; Relayed; Mon, 13 Feb 1995 09:50:03 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Mon, 13 Feb 1995 09:49:00 -0500 Date: Mon, 13 Feb 1995 09:49:00 -0500 X400-Originator: Karl.F.Moschner@urlus.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Mon Feb 13 09:49:48 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: Re: CCL:MNDO90 From: Karl.F.Moschner@urlus.sprint.com Message-ID: <"Mon Feb 13 09:49:48 199500*/I=F/G=Karl/S=Moschner/OU=4267EDUR/O=TMUS.URL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: ewing@jcvaxa.jcu.edu, chemistry@ccl.net Subject: Re: CCL:MNDO90 MIME-version: 1.0 Content-type: multipart/mixed; boundary="FnvcRBip3vl86vXDmktuZIQc9SnjE46r" --FnvcRBip3vl86vXDmktuZIQc9SnjE46r Content-type: text/plain; charset="us-ascii" > Who does one contact to buy MNDO90? > > Dave Ewing > John Carroll University > ewing@jcvaxa.jcu.edu I believe the latest version is MNDO93 and it's being distributed by Cray though, I belive, Molecular Simmulations had a distribution agreement with Cray for a short while. If I recall correctly, versions are available for Cray (naturally, and highly optimized), SGI and possibly IBM AIX but I don't know if it has been parallelized for SGI and IBM. Apparently, MNDOxx software/algorithm development is also ongoing as part of an EEC ESPRIT program (academic/government/industry consortium). Maybe Walter Thiel will get wind of this message and offer a brief update since, to my knowledge, he has only published MNDO(d) parameters for the halogens though more elements are supposedly included in MNDO93. Depending on your interests and need for semiempirical programs, you might also consider: Program(s) Contact MOPAC93/MOPAC V 7.0 QCPE qcpe@ucs.indiana.edu GEOMOS QCPE ZINDO Biosym contact local supplier/rep. Spartan Wavefunction support@wavefun.com Can anyone offer commentary/comparison of the semiempircal methods implemented in these programs? _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ --FnvcRBip3vl86vXDmktuZIQc9SnjE46r Content-type: text/plain; charset="us-ascii" --FnvcRBip3vl86vXDmktuZIQc9SnjE46r-- From RUSSO@FIS.UNICAL.IT Mon Feb 13 12:39:22 1995 Received: from csfisi.fis.unical.it for RUSSO@FIS.UNICAL.IT by www.ccl.net (8.6.9/930601.1506) id LAA28653; Mon, 13 Feb 1995 11:45:45 -0500 Date: Mon, 13 Feb 1995 17:50:42 +0100 (WET) From: RUSSO@FIS.UNICAL.IT Message-Id: <950213175042.202003c2@FIS.UNICAL.IT> Subject: again periodic boundary conditions To: chemistry@ccl.net X-Vmsmail-To: GMAIL::"chemistry@ccl.net" Hi Netters, I'm studying the conformational behaviour of small peptides of interest biological. Until now, the systems studied have been ob- tained by investigation MD at temperature constant and at energy constant, using the solvation model of a sphere. The program is Discover. I would like to know somethings more about the periodic boundary conditions used during the MD simulations of peptides, and if possible, the advantage using these conditions. Thanks in advance Tiziana From ramav@beloit.edu Mon Feb 13 13:14:31 1995 Received: from beloit.edu for ramav@beloit.edu by www.ccl.net (8.6.9/930601.1506) id MAA29372; Mon, 13 Feb 1995 12:19:55 -0500 Received: from macpost.beloit.edu by beloit.edu (AIX 3.2/UCB 5.64/4.03) id AA16220; Mon, 13 Feb 1995 11:19:52 -0600 Date: Mon, 13 Feb 1995 11:19:52 -0600 Message-Id: <9502131719.AA16220@beloit.edu> To: chemistry@ccl.net From: ramav@beloit.edu (Rama Viswanathan) Subject: UNIVIS:2D/3D VISUALIZATION PACKAGE FOR PC 486 MACHINES Forwarded at the request of Prof. S.R. GADRE >********************************************************************** > UNIVIS >********************************************************************** > Universal Visualization Package > > A universal 2D/3D visualization package, UNIVIS developed >by Professor Shridhar R. Gadre and Ajay Limaye at the Department of >Chemistry, University of Poona, Pune-411 007, INDIA is now available >for distribution. The package is currently available on PC 486 >platform with SVGA monitor and atleast 4 MB RAM. > > This unique package offers you the following features : >1. Normal visualization of molecules. >2. Data available on a 3D grid can be visualized in following ways : > a. Property textured on Van der Waals surface > b. Chicken wire plots > c. Property textured on any standard planes > d. Iso-valued surfaces with transparency effects > e. Any combination of the above. >3. Light & transparency effects. > > Such a rich package is not available on a comparable platform >(to the best of our knowledge and belief!). Of course, to see it is >to believe it! If interested in the package, contact >Professor Shridhar Gadre and a few sample graphics >screens will be sent to you. >.................................................................... > Professor Shridhar R. Gadre > Department of Chemistry > University of Poona, Pune-411007, INDIA. >e-mail gadre@unipune,ernet-in ; gadre@parcom.ernet.in >FAX : 0091-212-337551. > 0091-212-333899. >********************************************************************** > > Rama Viswanathan Dept. of Chemistry ramav@beloit.edu Beloit College, Beloit, Wisc. From GOMIDE@fapq.fapesp.br Mon Feb 13 13:40:53 1995 Received: from fapq.fapesp.br for GOMIDE@fapq.fapesp.br by www.ccl.net (8.6.9/930601.1506) id MAA00339; Mon, 13 Feb 1995 12:58:46 -0500 Date: Mon, 13 Feb 1995 15:56 BDB (-0200 C) From: gomide@fapq.fapesp.br Subject: Warning - possibly undelivered mail. Sender: Alberto Courrege Gomide To: segalemb@bruspvm.bitnet, chemistry@ccl.net, segalemb@bruspvm.bitnet Reply-to: gomide@fapq.fapesp.br Message-id: X-Envelope-to: chemistry@ccl.net X-VMS-To: IN%",chemistry@ccl.net,segalemb@bruspvm.bitnet" References: ANSP Network HEPnet SPAN Bitnet Internet gateway Comments: @FAPQ.FAPESP.BR - @FAPQ%FPSP.HEPNET - @BRFAPQ.BITNET - .BR gateway TAGB BRUSPVM MAILER 50 W=MAILER  HELO OHSTBH.BITNET  TICK 1313  MAIL FROM:  RCPT TO:  DATA  Received: from www.ccl.net by phem3.acs.ohio-state.edu (PMDF V4.2-13   #5888) id <01HMOBADKHCG8Y8VH5@phem3.acs.ohio-state.edu>; Sun,   5 Feb 1995 03:01:23 EDT  Received: for chemistry-request@ccl.net by www.ccl.net   (8.6.9/930601.1506) id CAA11755; Sun, 5 Feb 1995 02:43:59 -0500  Received: from sn01.sncc.lsu.edu for CHMORA@LSUVAX.SNCC.LSU.EDU by   www.ccl.net (8.6.9/930601.1506) id CAA11311; Sun,   5 Feb 1995 02:04:38 -0500  Received: from LSUVAX.SNCC.LSU.EDU by LSUVAX.SNCC.LSU.EDU (PMDF V4.2-14 #3426)   id <01HMO79NEOPO8WY7I2@LSUVAX.SNCC.LSU.EDU>; Sun, 5 Feb 1995 01:06:55 CST  Date: Sun, 05 Feb 1995 01:06:55 -0600 (CST)  From: CHMORA@LSUVAX.SNCC.LSU.EDU  Subject: CCL:Mopac and electron densities.  Sender: Computational Chemistry List  To: chemistry@ccl.net  Errors-to: ccl@ccl.net  Message-id: <01HMO79NEOPQ8WY7I2@LSUVAX.SNCC.LSU.EDU>  X-Envelope-to: SEGALEMB@BRUSPVM.BITNET  X-VMS-To: IN%"chemistry@ccl.net"  Content-transfer-encoding: 7BIT  Precedence: bulk    Dear colleagues:    I'm using MOPAC6 to calculate the atomic electron density in indole.  I found that the atomic electron densities calculated by MOPAC are quite differe   nt from those  reported in the literature (Theoret. Chim. Acta, 1970, 16, 22-32). For instance,   Mopac reports  that the electron density for the N atom in indole is 5.2213 (using AM1) while t   he one reported  in the literature is 1.69.  Could anybody please tell me why the huge difference?  I'll post a summary.    Thanks a lot in advance.    Guillermo.    ===============================================================================  Guillermo A. Morales Phone:(504) 388-2706  Chemistry Department Fax: (504) 388-3458  Louisiana State University  Baton Rouge, LA. 70803-1804 E-mail: chmora@sn01.sncc.lsu.edu  U.S.A.  ===============================================================================  ===============================================================================  ========= ============  ======== /// //////// /// /// =============  ======= /// /// /// /// ==============  ====== /// //////// /// /// ===============  ===== /// /// /// /// ================  ==== /////// //////// ///////// =================  === ==================  ===============================================================================  ===============================================================================      -------This is added Automatically by the Software--------  -- Original Sender Envelope Address: CHMORA@LSUVAX.SNCC.LSU.EDU  -- Original Sender From: Address: CHMORA@LSUVAX.SNCC.LSU.EDU  CHEMISTRY@ccl.net -- everyone | CHEMISTRY-REQUEST@ccl.net -- coordinator  MAILSERV@ccl.net: HELP CHEMISTRY | Gopher: www.ccl.net 73  Anon. ftp www.ccl.net | CHEMISTRY-SEARCH@ccl.net -- archive search  http://www.ccl.net/chemistry.html | for info send: HELP SEARCH to MAILSERV    .  QUIT From steve@carbo.chem.binghamton.edu Mon Feb 13 14:39:43 1995 Received: from carbo.chem.binghamton.edu for steve@carbo.chem.binghamton.edu by www.ccl.net (8.6.9/930601.1506) id OAA01771; Mon, 13 Feb 1995 14:31:06 -0500 Received: by carbo.chem.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA04549; Mon, 13 Feb 95 14:29:30 -0500 Date: Mon, 13 Feb 1995 14:19:43 -0500 (EST) From: Steven Schafer Subject: Q: SYBYL & Solvaetd Dynamics To: chemistry@ccl.net Cc: sybyl@extreme.chem.rpi.edu Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Do any of you Sybyl users know if there is a way that you can minimize the disk space required for a solvated dynamics run by storing only the data for the solvated molecule? I am interested only in the conformational changes in the solvated molecule and do not care about the included water molecules. Also I dump the coordinate file to calculate the optical rotation of the solvated molecule, and the waters make it very slow to read threw the dumped file. Thanks in advance, Steven E. Schafer S.U.N.Y. Binghamton Chemistry Department http://chemiris.chem.binghamton.edu:8080 Binghamton, New York USA From david@iris.claremont.edu Mon Feb 13 15:39:36 1995 Received: from iris.claremont.edu for david@iris.claremont.edu by www.ccl.net (8.6.9/930601.1506) id NAA01078; Mon, 13 Feb 1995 13:49:42 -0500 Received: (from david@localhost) by iris.claremont.edu (8.6.9/8.6.6) id TAA11491 for chemistry@ccl.net; Mon, 13 Feb 1995 19:01:52 GMT From: "David H." Message-Id: <199502131901.TAA11491@iris.claremont.edu> Subject: New WWW site with Hypermail archive of CCL To: chemistry@ccl.net Date: Mon, 13 Feb 1995 11:01:50 -0800 (PST) X-Mailer: ELM [version 2.4 PL20] Content-Type: text Content-Length: 1279 The Medicinal Chemistry Project, in conjuction with Biobyte Corp. and Pomona College, is pleased to announce a new chemistry World Wide Web server. Home page URL is: (those without hostname lookup use '134.173.4.161') http://medchem.claremont.edu/ Of special interest to readers of CCL is the searchable Hypermail archive of CCL, covering 1991 to date (updated daily). Also available: searchable QSAR archive (6,000 sets, both biological and physical-organic) searchable names archive (37,000 names/30,000 SMILES) detailed examples and documentation for Dr. Al Leo's CLOGP algorithm SW vendor information (just Biobyte Corp. and Daylight CIS currently) Note: To do any searching, you will need a 'forms' capable WWW browser. If you find this service useful, or if there is anything we can do to improve it, please let us know (email to webmaster@medchem.claremont.edu). -- David Hoekman Biobyte Corp. 645 N. College Ave. 201 West 4th St. Suite 204 Claremont, CA 91711 Claremont, CA 91711 Phone 909-624-5509 909-624-5992 FAX 909-624-5509 909-624-1398 Email david@medchem.claremont.edu biobyte@medchem.claremont.edu From steve@carbo.chem.binghamton.edu Mon Feb 13 16:39:33 1995 Received: from carbo.chem.binghamton.edu for steve@carbo.chem.binghamton.edu by www.ccl.net (8.6.9/930601.1506) id QAA05061; Mon, 13 Feb 1995 16:28:03 -0500 Received: by carbo.chem.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA04675; Mon, 13 Feb 95 16:26:04 -0500 Date: Mon, 13 Feb 1995 16:22:48 -0500 (EST) From: Steven Schafer Subject: Re: Q:Crystal Structures To: Jan Radomski Cc: chemistry@ccl.net In-Reply-To: <9502132028.AA15068@tiger.chem.uw.edu.pl> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 13 Feb 1995, Jan Radomski wrote: > > ----- > Steve, > > there is something amis in your structures: > Methyl-3,6-alpha-D-mannopyranoside > Methyl-3,6-beta-D-mannopyranoside > Methyl-3,6-beta-D-glucopyranoside > Methyl-3,6-beta-D-galactopyranoside > > are these items you're looking for in fact 3,6-di-O-methyl derivs? > > Jan > Jan, I accidently omitted "anhydro", they are methyl-3,6-anhydro pyranosides. Sorry for any confusion. Thanks for the response. Steven E. Schafer S.U.N.Y. Binghamton Chemistry Department http://chemiris.chem.binghamton.edu:8080 Binghamton, New York USA From ivarm@boc.ic.ee Mon Feb 13 16:48:37 1995 Received: from argus.chemnet.ee for ivarm@boc.ic.ee by www.ccl.net (8.6.9/930601.1506) id LAA28477; Mon, 13 Feb 1995 11:39:40 -0500 Received: from boc.ic.ee (boc.ic.ee [193.40.63.200]) by argus.chemnet.ee (8.6.9/8.6.9) with SMTP id SAA00568 for ; Mon, 13 Feb 1995 18:22:02 +0200 Received: from argus.chemnet.ee by boc.ic.ee id aa03978; Mon, 13 Feb 95 18:34:24 estonia From: "Ivar Martin" Date: Mon, 13 Feb 95 18:33:34 EST Message-Id: <1023.ivarm@boc.ic.ee_POPMail/PC_3.2.2> Reply-To: X-POPmail-Charset: English To: chemistry@ccl.net Subject: summary: conformer generator Dear CCL people, I asked you about programs which would generate a large variety of conformations as input for MOPAC 6.0 which I currently use. Several people asked me to share the answers with them, so I give you a summary. In addition to current responses I found from CCL archieves: - MOLGEN for PC - PowerSearch for MS-Windows from Tripos very many good words about - MacroModel - DGEOM from QCPE I would like to thank everyone who responded, namely Peter Burk Bill Ross E. Lewars Brian T. Luke Karl F.Moschner Jerzy Rudzinski Chris L. Waller Mike Tennant Andy Holder ==================================================================== My original question was: please suggest me a program which takes up the given geometry (cartesian or internal) and generates a lot of conformers from that for the MOPAC input. It would be nice if the program works in UNIX. (FORTRAN source would be excellent). Thank you! _______________________________ Dr. Ivar Martin Department of Bioorganic Chemistry tel: +372 2 526510 Institute of Chemistry fax: +372 2 536371 Akadeemia tee 15 EE0026 e-mail: ivarm@boc.ic.ee Tallinn, ESTONIA ===================================================================== ANSWERS in chronological order: ------------------------------------------------------- From: Peter Burk [my free translation into english... I.Martin] Dear Ivar, I have the perl's script which does the job you need. Only it is not very smart - it doesn't check the identical geometries and interatomic distances. -- Peeter Burk, Ph.D. Jakobi 2, EE2400 Tartu, Estonia Institute of Chemical Physics Phone (372-7) 441-453 Tartu University Fax (372-7) 441-453 Estonia E-mail peeter@chem.ut.ee ------------------------------------------------------------------- From: ross@cgl.ucsf.EDU (Bill Ross ) A recent CCL post mentioned using Amber for generating a spectrum of conformations using high-temperature molecular dynamics; in case you are interested in this option, here is the Amber info. There is a mail reflector for Amber users and people interested in Amber. A major part of the traffic is the bugfix announcements. amber@cgl.ucsf.edu amber@ucsfcgl.bitnet and mail to either amber-request@cgl.ucsf.edu amber-request@ucsfcgl.bitnet for administrative requests. Bill Ross -------------------------------------------------------------------- From: "E. Lewars" The PC program pcGlobal generates a set or conformers randomly (stochastically). The program is sold by Serena Software, Box 3076, Bloomington,IN 47402-3076. Email: GILBERT@ucs.indiana.edu Kevin Gilbert, President. The program Spartan will search through the possible conformers and calc their energies; Spartan is UNIX-based and has MM, ab in., and semiemp. Contact Wavefunction, Inc, 18401 von Karman, Suite 210, Irvine, CA 92715 USA. Email SALES@WAVEFUN.COM or SUPPORT@WAVEFUN.COM -------------------------------------------------------------------- From: btluke@VNET.IBM.COM Dr. Martin, When I ported MOPAC7 from a Sun to the IBM RS/6000, I modified it so that it will generate multiple initial conformations of a molecule >from a single input file (see Journal of Computational Chemistry, 15 (1994) 1176-1185). If this will fit your needs, you can order the program from the Quantum Chemistry Program Exchange (QCPE). Brian T. Luke, Ph.D. -------------------------------------------------------------------- From: Karl.F.Moschner@urlus.sprint.com I have used the conformational search routines in the commercial package Sybyl to generate conformers and then submit the individual structures for single point calculations using MOPAC V6.0. You could also use any other 3rd party package for which they provide an interface or create your own using macros. Unfortunately, they're unlikely to provide the source code. _______________________________________________________________________ / \ | Comments are those of the author and not Unilever Research U. S. | | | | Karl F. Moschner, Ph. D. | | | | Unilever Research U. S. e-mail: Karl.F.Moschner@urlus.sprint.com | | 45 River Road Phone: (201) 943-7100 x2629 | | Edgewater, NJ 07020 FAX: (201) 943-5653 | \_______________________________________________________________________/ ------------------------------------------------------------------------ From: Jerzy Rudzinski Dear Dr Martin, Thare are commercial packages that do the job. For sure I know two that is ANCHOR II from Fujitsu Limited (good for SUN and some other UNIX machines) and Spartan. I am sure other commercial programs can also do. If you get responces, please share the info. I am also interested in good conformational generators. Wishes, Jerzy Rudzinski ----------------------------------------------------------------------- From: "Dr. Chris L. Waller" I have an SPL (Sybyl Programming Language) script which does exactly what you desire. The only catch is - you must have Sybyl to run it. If you can use it, I will gladly send a copy. ******************************************************************** *Chris L. Waller, Ph.D. PHONE 919-541-7976* *Research Chemist FAX 919-541-5394* *waller@thor.herl.epa.gov * *Pharmacokinetics Branch (MD-74) * *ETD/HERL/USEPA * *Research Triangle Park, NC 27711 * * * *Disclaimer: Mention of trade names or products does not constitute* *endorsement by the United States Environmental Protection Agency. * ******************************************************************** ---------------------------------------------------------------------- From: Mike Tennant Ivar, you can use macromodel to generate a set of unique conformations and then extract these confs to individual mopac input files using babel. Both progs run under unix. Mike --------------------------------------------------------------------- From: Andy Holder Dear Dr. Martin, The simulated annealing subroutine in our AMPAC 5.0 with Graphical User Interface is designed to help with this problem rather directly. The algorithm generates candidate conformers and optimizes them in AMPAC using our advanced convergence algorithms. The method keeps up with previous located structures and discards duplicates. It also has a number of nice penalty features that eliminate poor candidates early on. The methodology is "annealing" only in the conformer generation step. The sorting and grouping step is very intelligent and is built around some literature heuristic algorithm methods. The GUI also collects and organizes the results in a nice graphics window. We are currently running a demonstration promotion, so if anyone would like to try it out, get in touch with me as noted below. Andy Holder =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= DR. ANDREW HOLDER President, Semichem Semichem, Inc. || Internet Addr: aholder@cctr.umkc.edu 7128 Summit || Phone Number: (913) 268-3271 Shawnee, KS, 66216 || FAX Number: (913) 268-3445 =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From steve@carbo.chem.binghamton.edu Mon Feb 13 17:39:28 1995 Received: from carbo.chem.binghamton.edu for steve@carbo.chem.binghamton.edu by www.ccl.net (8.6.9/930601.1506) id RAA06433; Mon, 13 Feb 1995 17:18:49 -0500 Received: by carbo.chem.binghamton.edu (931110.SGI/931108.SGI.ANONFTP) for chemistry@ccl.net id AA04863; Mon, 13 Feb 95 17:17:14 -0500 Date: Mon, 13 Feb 1995 17:15:18 -0500 (EST) From: Steven Schafer Subject: Q: SYBYL & Solvaetd Dynamics (fwd) To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Do any of you Sybyl users know if there is a way that you can minimize the disk space required for a solvated dynamics run by storing only the data for the solvated molecule? I am interested only in the conformational changes in the solvated molecule and do not care about the included water molecules. Also I dump the coordinate file to calculate the optical rotation of the solvated molecule, and the waters make it very slow to read threw the dumped file. Thanks in advance, Steven E. Schafer S.U.N.Y. Binghamton Chemistry Department http://chemiris.chem.binghamton.edu:8080 Binghamton, New York USA p.s. This is the second time I have sent this. I did not recieve a conformation of it being recieved. Sorry if anyone gets this twice. From CHMORA@LSUVAX.SNCC.LSU.EDU Mon Feb 13 17:43:24 1995 Received: from sn01.sncc.lsu.edu for CHMORA@LSUVAX.SNCC.LSU.EDU by www.ccl.net (8.6.9/930601.1506) id RAA06849; Mon, 13 Feb 1995 17:34:38 -0500 Received: from LSUVAX.SNCC.LSU.EDU by LSUVAX.SNCC.LSU.EDU (PMDF V4.2-14 #3426) id <01HN0A33QI008WY77P@LSUVAX.SNCC.LSU.EDU>; Mon, 13 Feb 1995 16:36:51 CST Date: Mon, 13 Feb 1995 16:36:51 -0600 (CST) From: CHMORA@LSUVAX.SNCC.LSU.EDU Subject: Differences between MOPAC 6 and MOPAC 7 To: chemistry@ccl.net Message-id: <01HN0A33QI028WY77P@LSUVAX.SNCC.LSU.EDU> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters: Could somebody please tell me the difference between MOPAC 6 and MOPAC 7? As always, I'll summarize the answers. Thanks a lot in advance. Sincerely, Guillermo A. Morales =============================================================================== Guillermo A. Morales Phone:(504) 388-2706 Chemistry Department Fax: (504) 388-3458 Louisiana State University Baton Rouge, LA. 70803-1804 E-mail: chmora@sn01.sncc.lsu.edu U.S.A. =============================================================================== =============================================================================== ========= ============ ======== /// //////// /// /// ============= ======= /// /// /// /// ============== ====== /// //////// /// /// =============== ===== /// /// /// /// ================ ==== /////// //////// ///////// ================= === ================== =============================================================================== ===============================================================================