From chemistry-request@server.ccl.net Fri Dec 22 01:44:59 2000 Received: from century.fen.bilkent.edu.tr (century.fen.bilkent.edu.tr [139.179.97.100]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id BAA24646 for ; Fri, 22 Dec 2000 01:44:57 -0500 Received: from pinar (pinar [139.179.97.99]) by century.fen.bilkent.edu.tr (8.9.1/8.9.1) with ESMTP id IAA18538; Fri, 22 Dec 2000 08:44:17 +0200 (EET) Date: Fri, 22 Dec 2000 08:49:38 +0200 (EET) From: Ulrike Salzner X-Sender: salzner@pinar To: sergiusz kwasniewski cc: chemistry@ccl.net Subject: Re: CCL:bandgap from UV/Vis spectra In-Reply-To: <200012211056.LAA31642@alpha.luc.ac.be> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Sergiusz, a motivation for taking the onset of absorption as the band gap might be that at this point the electrons are starting to enter the conduction band. The onset of photocurrent, for instance, is below the maximum of absorption. In polyacetylene the onset of absorption coincides with the onset of photocurrent at about 1.48 eV, while the absorption maximum occurs at 1.7 eV. Therefore in solid state physics, the onset of absorption might simply be a more interesting point than the absorption maximum. The absorption maximum could be shifted due to a higher energy because of a higher density of states at a position different from the band edge. Furthermore, excitons play a role for many systems. I don't know who used the onset of absorption first but the above data are from Tani et al. Solid State Communications, 1980, 33, 499-503. Best wishes, Ulrike Salzner =================================================================== Dr. Ulrike Salzner Associate Professor Department of Chemistry Tel.: (312) 290-2122 Bilkent University Fax.: (312) 266-5097 06533 Bilkent, Ankara e-mail: salzner@fen.bilkent.edu.tr Turkey ==================================================================== On Thu, 21 Dec 2000, sergiusz kwasniewski wrote: > Hi, > > we're trying to 'guess' a bandgap from our calculated > UV/Vis spectra, but instead of using the first peak > maximum (lowest energy) I've heard that experimentalists > working on polymers take the crossing of the tangient > at the point of inflection at the low energy side. > > Now my question is if someone knows why they proceed > like this and more importantly where I can find a > reference about this ? > > Thanks in advance .. I'll summarize if someone would > be interested in this .. > > Sergiusz > > > ___________________________________________________ > > Sergiusz Kwasniewski > LUC SBG/TS > Universitaire Campus Gebouw D > 3590 Diepenbeek > BELGIUM > > tel(direct): 032 (0)11/268315 > fax : 032 (0)11/268301 > email : sergiusz.kwasniewski@luc.ac.be > http://www.luc.ac.be/Research/TheoChem > ___________________________________________________ > > > -= 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 > > > > > > From chemistry-request@server.ccl.net Fri Dec 22 11:11:09 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27693 for ; Fri, 22 Dec 2000 11:11:08 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id LAA30663; Fri, 22 Dec 2000 11:10:52 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 22 Dec 2000 11:09:59 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G5Z0040L8S0U7@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 22 Dec 2000 11:07:12 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 22 Dec 2000 11:10:20 -0500 Content-return: allowed Date: Fri, 22 Dec 2000 11:10:11 -0500 From: "Shobe, Dave" Subject: qcisd vs ccsd vs bd To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAAB7C@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Apparently the copper monohalides' wavefunctions are more "interesting" than I expected...I found about half a dozen articles on the subject. But in general: What are the pros and cons of the qcisd, ccsd, and bd methods (and the corresponding (t) methods)? Does one usually employ ccsd or bd only when qcisd misbehaves, or has misbehaved for similar molecules? ("Misbehavior" including the triples correction problem I mentioned earlier, inability to achieve convergence, etc.) Or are there cases when one can a priori suspect that qcisd might not give accurate results? --David Shobe From chemistry-request@server.ccl.net Fri Dec 22 11:46:10 2000 Received: from oc30.uni-paderborn.de (oc30.uni-paderborn.de [131.234.240.90]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27880 for ; Fri, 22 Dec 2000 11:46:09 -0500 Received: from localhost (cpilger@localhost) by oc30.uni-paderborn.de (SGI-8.9.3/8.9.3) with ESMTP id SAA04730; Fri, 22 Dec 2000 18:31:16 +0100 (CET) Date: Fri, 22 Dec 2000 18:31:16 +0100 From: Christian Pilger To: amber@cgl.ucsf.edu cc: chemistry@ccl.net Subject: froce field parameters In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear colleagues, in my current project I have been working with AMBER 6.0. I try to calculate the energies of binding of different orientations of a small moelcule within a protein. Though AMBER contains a lot of parameters for non-protein atoms, the variety of my small molecule is not entirely covered. As I don't have enough experience to parameterize the missing bonds, angles, and dihedrals on my own, I was thinking of taking these from the MMFF94. I could imagine two ways: 1. to borrow only those parameters for the small molecule, that are missing within AMBER, applying some scaling to the force constants 2. to use the MMFF94-parameters for the entire small molecule without any scaling, while treating the protein with the AMBER parameters Concerning the electrostatics I intend to stay with the AMBER philosophy, employing the RESP methodology. At the initial stage, I'm just interested in calcualting relative energies, i.e. rank different conformations/orientations of the same inhibitor with a given protein conformation. Do you think, such a strategy would be reasonable ? Any comments are welcome. Merry X-mas & guten Rutsch, Christian ----------------------------------------------------------------- Dr. Christian Pilger Istituto di Strutturistica Chimica "Giordano Giacomello" C.N.R. - Sezione di Trieste Area Science Park - Basovizza Strada Statale 14 - Km. 163.5 I-34012 Trieste/Italy Tel.: +39+040+226881 Fax : +39+040+9221126 e-mail: cpilger@oc30.uni-paderborn.de ----------------------------------------------------------------- From chemistry-request@server.ccl.net Fri Dec 22 07:36:16 2000 Received: from mailgw.barc.ernet.in ([202.54.18.131]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id HAA26963 for ; Fri, 22 Dec 2000 07:36:14 -0500 Received: from apsara.barc.ernet.in (apsara.barc.ernet.in [192.168.1.21]) by mailgw.barc.ernet.in (8.9.3/8.9.3) with ESMTP id SAA07215 for ; Fri, 22 Dec 2000 18:13:23 +0530 (IST) (envelope-from tapang@apsara.barc.ernet.in) Received: from localhost (tapang@localhost) by apsara.barc.ernet.in (8.9.3/8.9.3) with ESMTP id SAA30852 for ; Fri, 22 Dec 2000 18:12:24 +0530 Date: Fri, 22 Dec 2000 18:12:24 +0530 (IST) From: "Dr.Tapan K.Ghanty" To: chemistry@ccl.net Subject: SCSI CONTROLLER Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Friends, Merry Christmas & Happy New Year 2001 I have one hardware question. Which SCSI controller card will be better for PC-LINUX machine. I am sure many people, here in this list use PC-LINUX with SCSI hard disk. Anybody used ADAPTEC 2940 UW or ADAPTEC 19160 SCSI card for PC-LINUX? With thanks, Tapan K. Ghanty Theoretical Chemistry Section Chemistry Division BARC Trombay, Mumbai 400 085 India From chemistry-request@server.ccl.net Fri Dec 22 10:41:12 2000 Received: from mail1.uniroma1.it (mail1.uniroma1.it [151.100.4.5]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id KAA27567 for ; Fri, 22 Dec 2000 10:41:11 -0500 Received: from chilastre2 ([151.100.52.105]) by mail1.uniroma1.it (Lotus Domino Release 5.0.5) with SMTP id 2000122216384045:28745 ; Fri, 22 Dec 2000 16:38:40 +0100 Message-Id: <3.0.5.32.20001222164301.007cdc60@mail.uniroma1.it> X-Sender: molbeam@mail.uniroma1.it X-Mailer: QUALCOMM Windows Eudora Light Version 3.0.5 (32) Date: Fri, 22 Dec 2000 16:43:01 +0100 To: anna.giardini@uniroma1.it From: molbeam Subject: XIX MOLBEAM WEB PAGE Mime-Version: 1.0 X-MIMETrack: Itemize by SMTP Server on mail1/Uniroma1/it(Release 5.0.5 |September 22, 2000) at 22/12/2000 16.38.40, Serialize by Router on mail1/Uniroma1/it(Release 5.0.5 |September 22, 2000) at 22/12/2000 16.42.24, Serialize complete at 22/12/2000 16.42.24 Content-Type: text/plain; charset="us-ascii" Dear Colleagues, please visit the web page http://molbeam.chem.uniroma1.it/Molbeam on the XIX Molecular Beam Congress that is to take place in Rome June, 2001. A second circular will be sent to you in the middle of January. Best Regards, The organizing committee From chemistry-request@server.ccl.net Fri Dec 22 11:20:12 2000 Received: from ccl.net (atlantis.ccl.net [192.148.249.4]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27767 for ; Fri, 22 Dec 2000 11:20:12 -0500 Received: from krakow.ccl.net (krakow.ccl.net [192.148.249.195]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id LAA03373; Fri, 22 Dec 2000 11:19:56 -0500 (EST) Date: Fri, 22 Dec 2000 11:19:56 -0500 (EST) From: Jan Labanowski To: chemistry@ccl.net cc: jkl@ccl.net Subject: Merry Holidays and a Happy New Year to all Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Merry Holidays and All the Best in 2001 from CCL Team. Be happy, hope for better, keep your spirits high, and take care of your body since mind cannot exist without the well functioning support services... ------------------------------------------------------------------------------- + ! XXX ! XXXXX ! XXXXXXX ! XXXXXXXXX ! "BOAS FESTAS" ! "JOYEUX NOEL" \ / * ! "VESELE VANOCE" --O-- XXX ! "MELE KALIKIMAKE" / \ "HOME" ! "NODLAG SONA DHUIT" "PEACE." ! "BLWYDDYN NEWYDD DDA" "BON NADAL." ! "GOD JUL" "BOLDOG UJ EVET" ! "BUON ANNO" \ / "CHANUKAH SAMEACH" ! \ / "FELIZ NATAL" --O-- "DOSIEGO!" ! --O-- "FELIZ NAVIDAD" / \ "HAPPY HANUKKAH" ! / \ "KALA CHRISTOUGENA" "PARI ARTSAGOURT" ! "VROLIJK KERSTFEEST" "KELLEMES UNNEPEKET" ! "FROEHLICHE WEIHNACHTEN" "NAYA VARSH SHUBH HO" ! "BUON NATALE-GODT NYTAR" "ATHBHLIAIN FAOI MHAISE ! "HUAN YING SHENG TAN CHIEH" "IYI YILLAR-HYVAEAE LOMAA ! "WESOLYCH SWIAT-SRETAN BOZIC" \ / "NA ZDOROVE" ! "MOADIM LESIMHA-LINKSMU KALEDU" --O-- "MERRY CHRISTMAS" ! "HAUSKAA JOULDA-AID SAID MOUBARK" / \ "FELICHAN JARFINON" ! "'N PRETTIG KERSTMIS" "#-SHUB NAYA BARAS-@" ! "ONNELLISTA UUTTA VUOTTA" ! "INPAKARAMAANA VIDUMURAI! "Z ROZHDESTVOM KHRYSTOVYM" >+< "STASTNY NOVY ROK-CHEERS!! "NADOLIG LLAWEN-GOTT NYTTSAR" ! "CHING CHI SHEN TAN-@@@@@!! "CRACIUN FERICIT-GOJAN KRISTNASKON" *** **!! ! "S NOVYM GODOM-FELIZ ANO NUEVO" .-'-. mmmmmm !!!! ! "GLEDILEG JOL-NOELINIZ KUTLU OLSUM" .-' .-. '-.! ! xxxx ! "EEN GELUKKIG NIEUWJAAR-SRETAN BOSIC" .-' .-' '-. '-.! . ! "KRIHSTLINDJA GEZUAR-KALA CHRISTOUGENA" .-' '-. '-. ! "SELAMAT HARI NATAL - LAIMINGU NAUJU METU"' '-. '-. ! "SARBATORI FERICITE-BUON ANNO" ! ___________ !-..!- ! "ZORIONEKO GABON-HRISTOS SE RODI" ! !__o_!__!__! ! ! "BOLDOG KARACSONNY- VESELE VANOCE" ! !_ooo!__@__! ! ! "MERRY CHRISTMAS**JOY**HAPPY NEW YEAR" !ooooo__#__! ! (\_/)-=)) ! "ROOMSAID JOULU PUHI -KUNG HO SHENG TEN" . ! =('.')=// ! "FELICES PASUAS-EIN GLUCKICHES NEUEJAHR*.-.-' -.._________! ( ~~~ )/ ! "PRIECIGUS ZIEMAS SVETKUS SARBATORI VESLLE" '-.-''-.. `w---w` ! "BONNE ANNEE-BLWYDDYN NEWYDD DDA*FELIZ NATAL" '-.... ! SHENORAVOR SOORP TSENOONT,SHENORAVOR NOR DARI" ! EID MUBARAK -|- MALIGAYANG PASKO -|- GEZEELLIGE" ! KERSTMIS -|- CHRISTUJUMNA RUKSHUMMA -|- PIVDLUANA" ! JODLUME UKIOTARME-LO ~|~ HAUOLI MAKAHIKI HOU ~|~ " ! CHUC MUNG NGAY TROI SINH - CHUC MUNG NAM MOI--*--*-" ! HAPPY KWANZAA ~*~ NODLAIG MHAITH CHUGNOT*X*X*X*X*X*X" ! XXXXXX ! XXXXXX ! XXXXXX ! ------------------------------------------------------------------------------- I will add some thoughts under the holiday tree hoping that most of you will miss them (the tree grew so high -- please continue sending me additions). It is hard to write something on the occasion of entering a new millennium. I am not a prophet (I hope... {:-)}). But there is also a less heavy anniversary... The CCL will be 10 years old in January. On one hand it asks for celebrations, on the other hand, I wish that I could unveil something on this occasion saying: "The New CCL for The New Millenium". Unfortunately I have tons of ideas and very little time to implement any of them. The truth is that "something" has to pay my salary, and CCL does not. But I hope that this service is still very helpful as it is. Thank you for your good word and encouragement. It helps to hope that you do something useful. I want to use this occasion to thank the OSC management for 10 years of continuing support of CCL not only with equipment, space, and network access, but also for providing for students assistants. I also want to thank those of you, who support the CCL Development fund. This is very important for me not only because it brings money which I can use to support students assistants and partially reimburse OSC for hardware and software. It is also very important since it proves that there are some people who not only say "CCL is useful" but also bet their money on it. Thank you very much... If you did not contribute yet, please consider. Just send me a check as described in the page: http://www.ccl.net/chemistry/aboutccl/supporting The fact that I need your support is part of a much broader phenomenon. I see how my public radio station fights for support from the listeners. The same with public TV. When I go back to 15 years ago, they did not do so much advertising (woops... thanking) their supporters. They had the core support coming from private, public, and government foundations. This support actually is no longer adequate. We all realize that everything costs. Everything has to pay for itself. But it became so urgent in recent years. It is easy too see how much money goes to ever growing government bureaucracy (controller controlling controller of the controller who controls the manager of controllers) which makes sure that our taxes are spent equitably and legally. Yes, it gives work for many people and we have less unemployment, but this workforce could do something more useful than pushing paper and red tape on us. This is a general trend, and it seems to be everywhere. As an example... Poland, the country where I was born, is now free of communists, it joined the free market team. It is a democracy. At the same time, it has now about twice the amount bureaucrats compared to the worst period of communist regime (which is synonymous with bureaucracy). And the Parkinson's law is as valid as before. Why societies cannot make better use of their people but to put them at work to push paper? The same is visible everywhere, at each stage of the society. CCL is in a much better position with its steady support from OSC. However, it is a general situation that community services have to support themselves. The universities are no longer the idealized sites where people learn and teach. The better known universities nowadays are more like a non-profit research institutes supporting themselves through contracts. While their advertise their faculty as the best researchers in the nation, these faculty members rarely teach. They pay themselves out of this with "time release". At the same time there is a steady pressure from the public to make the scientists do something useful. The problem is that things which are really (really!!!) useful would be most likely dismissed by 99% of the public as "wasteful big science which does not result in the product" (which could have the potential to contribute to products which nobody yet dreamed off). At the same time we are quite guilty trivializing all what we do, and trying to tie it to "important practical applications" and "economic impact". There are some popular overviews of the dangers (see for example: "The Kept University" piece by Eyal Press and Jennifer Washburn published by Atlantic Monthly: http://www.theatlantic.com/cgi-bin/o/issues/2000/03/press.htm ) No, I am not against the corporate research. I actually think that you guys in corporate research do on average more research than people in academia (where we spend much of our time writing proposals and serving almighty bureaucracy rather than doing research). But the current status is quite uncomfortable for academia and corporate research. There are several major issues from my perspective: 1) Intellectual property (I know I will enrage many people, but the results of research done in academia should be in my humble opinion public domain. Oh yes, giving proper credit, or course, but research done at academia should not be patented or sold. But many of us are forced to do it to support their research. Our administrations see research as asset which can be sold. It is a big change from say 30 years ago, when research results coming from academia were just a proof of competent faculty. And in some places, when you publish something which is patentable and do not work secure patent for this, you may be in trouble. At the same time, we now patent genes which God gave us, and algorithms, i.e., mathematics. Where it will stop? I understand that these are lucrative litigation areas, but it may be time to wake up. 2) The pressure for scientists to "earn" money. This forces faculty to look for research which actually brings revenues rather than things which are risky but exciting. In other words, the science done at academia is less and less "learning", but more and more contract work for commercial or political sector. The collaboration between academia and corporate research suffers (since many corporate scientists wanting to collaborate with their academic colleagues face the question: "OK, how much you can give me", while we all know that the corporate scientists are not the ones who hold purses). At the same time, scientists relying on government support have to produce "success stories" (i.e., photo or media opportunities) for politicians rather than focus on the important problems which do not tie nicely to: "We save lifes", "We drive the economic progress", "We make our country powerful". Not that it is bad, but technology transfer is the last, not the first step in scientific research. Not all science is engineering... 3) The requirement to be productive. Many people choose to publish the same paper over and over again to show "contribution" rather than think about something really new to learn and do, or just about passing their body of knowledge to students either by teaching or by publishing a book. It is not an exaggeration to say that "success" at the research university is essentially the amount of overhead brought from extramural funding (make no mistakes, the equipment is a problem, since it takes space and money to operate, unless it also attract additional funding). The transition from tenure-track to tenure in research universities depends on the support acquisition success stories. Also, the changes in tenure system which essentially scrapped the security of academic positions makes you wonder how academic freedom is defined. The underlying assumption is that there is a peer review system which rewards the "productive", "constructive", and "innovative". I hope it works well all the time, but I reserve my doubts. Of course, some people may become unproductive with time if not stimulated by "evaluation". But we forgot one thing... Science is not a profession, it is a call from within. If you do not have this call, you should not practice it. You should not be a priest if you do not feel the constant need to get closer to God. You should not be a scientist if you do not want to offer your mind and body to science and join the harsh convent. Only those of us who are true believers should be admitted to the chosen group of higher priests (tenure). Unfortunately, the criteria for granting tenure do not probe these virtues and seem often to stress the expediency. Let us hope that these clouds will disappear and the Sun will shine again. In short: For all of us, more stability and opportunity to do what we believe in. Let us hope that the turbulent economic times can be avoided. Let also hope that some of the brightest kids will try to choose science as profession rather than take "professional careers" like dentists, lawyers and managers. Best of Holidays, and Happy New Year for all of you Jan Labanowski jkl@ccl.net Jan K. Labanowski | phone: 614-292-9279, FAX: 614-292-7168 Ohio Supercomputer Center | Internet: jkl@ccl.net 1224 Kinnear Rd, | http://www.ccl.net/chemistry.html Columbus, OH 43212-1163 | http://www.ccl.net/ From chemistry-request@server.ccl.net Fri Dec 22 11:20:38 2000 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id LAA27779 for ; Fri, 22 Dec 2000 11:20:38 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id LAA12196; Fri, 22 Dec 2000 11:20:22 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Fri, 22 Dec 2000 11:19:29 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G5Z0042E97UU7@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Fri, 22 Dec 2000 11:16:42 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Fri, 22 Dec 2000 11:19:50 -0500 Content-return: allowed Date: Fri, 22 Dec 2000 11:19:47 -0500 From: "Shobe, Dave" Subject: gamess people play on the pc To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAAB7D@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 I'm considering downloading Gamess-US for Windows (even though it will probably take an entire day with my modem), because it has more multireference options that Gaussian. 1. Have any of you done this, and would you recommend it? 2. Are there utilities that can transfer information (basis sets, wavefunctions, etc.) between Gamess and Gaussian? 3. How do Gamess and Gaussian compare as regards time and resource use on a PC? --David From chemistry-request@server.ccl.net Fri Dec 22 13:07:23 2000 Received: from resstor.ndsu.nodak.edu (resstor.ndsu.NoDak.edu [134.129.111.204]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA28202 for ; Fri, 22 Dec 2000 13:07:22 -0500 Received: from hotmail.com (sud8b.pharm.ndsu.NoDak.edu [134.129.118.52]) by resstor.ndsu.nodak.edu (8.9.3/8.9.3) with ESMTP id MAA18917; Fri, 22 Dec 2000 12:06:33 -0600 Message-ID: <3A4397D5.6C43FA05@hotmail.com> Date: Fri, 22 Dec 2000 12:05:09 -0600 From: xin_hu Organization: NDSU X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Christian Pilger CC: amber@cgl.ucsf.edu, chemistry@ccl.net Subject: Re: CCL:froce field parameters References: Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Hi, Christian: Would you please give the details about the MMFF94. I like your idea. How do you think about the Zn ? xin Christian Pilger wrote: > Dear colleagues, > > in my current project I have been working with AMBER 6.0. I try to > calculate the energies of binding of different orientations of a small > moelcule within a protein. Though AMBER contains a lot of parameters for > non-protein atoms, the variety of my small molecule is not entirely > covered. As I don't have enough experience to parameterize the missing > bonds, angles, and dihedrals on my own, I was thinking of taking these > >from the MMFF94. > > I could imagine two ways: > > 1. to borrow only those parameters for the small molecule, that are > missing within AMBER, applying some scaling to the force constants > > 2. to use the MMFF94-parameters for the entire small molecule without any > scaling, while treating the protein with the AMBER parameters > > Concerning the electrostatics I intend to stay with the AMBER philosophy, > employing the RESP methodology. > > At the initial stage, I'm just interested in calcualting relative > energies, i.e. rank different conformations/orientations of the same > inhibitor with a given protein conformation. > > Do you think, such a strategy would be reasonable ? > > Any comments are welcome. > > Merry X-mas & guten Rutsch, > > Christian > > ----------------------------------------------------------------- > > Dr. Christian Pilger > > Istituto di Strutturistica Chimica "Giordano Giacomello" > C.N.R. - Sezione di Trieste > Area Science Park - Basovizza > Strada Statale 14 - Km. 163.5 > I-34012 Trieste/Italy > > Tel.: +39+040+226881 > Fax : +39+040+9221126 > e-mail: cpilger@oc30.uni-paderborn.de > > ----------------------------------------------------------------- > > -= 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 -- ************************************************* Xin Hu Department of Pharmaceutical Science College of Pharmacy North Dakota State University Fargo, ND 58105 Tel: 701-231-8298 (O) 701-231-4360 (H) Fax: 701-231-7781 E-mail: Xin_Hu@ndsu.nodak.edu xxh0541@hotmail.com *************************************************