From chemistry-request@server.ccl.net Thu Oct 31 03:16:26 2002 Received: from tigris.klte.hu ([193.6.138.33]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9V8GPf18618 for ; Thu, 31 Oct 2002 03:16:26 -0500 Received: from cthulhu (193.6.133.59) by tigris.klte.hu (MX V5.1-A Vn6f) with SMTP; Thu, 31 Oct 2002 09:16:54 +0200 Message-ID: <002c01c280b6$2f5d92e0$3b8506c1@cthulhu> From: "Tamas E. Gunda" To: "Peter Gannett" , References: Subject: Re: CCL:calculate tau (out of plane displacement) Date: Thu, 31 Oct 2002 09:19:07 +0100 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 Hi, Do you actually mean pyramidality, don't? The out-of-plane displacement is not the best measure, as it depends on the bond lengths. For different possibilities (such as POAV or P index) have a look at http://www.compuchem.com/m2m2.htm Tamas Dr. Tamas E. Gunda University of Debrecen, H-4010 Debrecen, Hungary tamasgunda@tigris.klte.hu ----- Original Message ----- From: "Peter Gannett" To: Sent: Wednesday, October 30, 2002 22:49 Subject: CCL:calculate tau (out of plane displacement) > Hi > > I'm trying to calculate tau, the out of plane displacement for a > central atom to which three others are attached (eg for I-J-K-L, K is > the central atom, I, J, L are attached), assuming you know all bond > lengths between K and the attached atoms and all angles (I-K-L, etc). I > have made a weak attempt at coming up with this but since this value is > often reported (without reference as to how it was determined/calc) I > was hoping that someone had the necessary equations to figure this out. > Thanks. > > Pete > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > From chemistry-request@server.ccl.net Thu Oct 31 06:28:44 2002 Received: from sina.com ([202.108.35.252]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9VBShf24364 for ; Thu, 31 Oct 2002 06:28:43 -0500 Received: (qmail 26981 invoked by uid 99); 31 Oct 2002 11:25:25 -0000 Message-ID: <20021031112525.26980.qmail@sina.com> From: chenghuiqc To: chemistry@ccl.net Subject: About constant velocity MD in VASP MIME-Version: 1.0 Date: Thu, 31 Oct 2002 19:25:25 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Dear Sir: I have a question about the VASP program. I want to know if I can keep some atom velosities constant and leave the others in free dynamic motion when I use the constant velocity MD function in VASP. How can I get this goal? Thank you Dept chemistry Nanjing Univ P.R.China ______________________________________ =================================================================== 免费试用新浪15M收费邮箱 赶紧行动！ (http://vip.sina.com/sol_mail/promotion/pro_men.html) 新浪二手市场：一元投入，十分惊喜，百分满意 (http://classad.sina.com.cn/2shou/) 数万张手机图片数万首短信铃声任你挑选，每天都有更新 (http://sms.sina.com.cn/cgi-bin/sms/smspic.cgi) From chemistry-request@server.ccl.net Thu Oct 31 05:08:22 2002 Received: from mailgate.rz.uni-karlsruhe.de ([129.13.64.97]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VA8Lf22025 for ; Thu, 31 Oct 2002 05:08:21 -0500 Received: from rz70.rz.uni-karlsruhe.de (rz70.rz.uni-karlsruhe.de [129.13.97.243]) by mailgate.rz.uni-karlsruhe.de with esmtp (Exim 3.36 #1) id 187CFH-0000IS-00; Thu, 31 Oct 2002 11:08:11 +0100 Date: Thu, 31 Oct 2002 11:08:10 +0100 (CET) From: Harald Svedung To: "Tamas E. Gunda" cc: Peter Gannett , Subject: Re: CCL:calculate tau (out of plane displacement) In-Reply-To: <002c01c280b6$2f5d92e0$3b8506c1@cthulhu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id g9VA8Mf22026 Hi, To be specific, in case someone should still want to get the out-of-plane hight: c out-of-plane distance opr11=q(4)-q(4) x origin corner (opr is distance, q is position) opr12=q(5)-q(5) y opr13=q(6)-q(6) z opr21=q(10)-q(4) x right leg corner opr22=q(11)-q(5) y opr23=q(12)-q(6) z opr31=q(7)-q(4) x left leg corner opr32=q(8)-q(5) y opr33=q(9)-q(6) z opr41=q(1)-q(4) x top corner opr42=q(2)-q(5) y opr43=q(3)-q(6) z opl=(opr41*(opr22*opr33-opr23*opr32)- opl is out-of-plane & opr42*(opr21*opr33-opr23*opr31)+ & opr43*(opr21*opr32-opr22*opr31))/ & dsqrt((opr22*opr33-opr23*opr32)**2+ & (opr21*opr33-opr23*opr31)**2+ & (opr21*opr32-opr22*opr31)**2) this is the projection of the vector from the origin to the top onto the normal vector of the plane spaned by the two legs. I've used this in potential functions used at low energies. I guess, at higher energies one has to care about coupling to other bond length related modes. take care! :-) /Harald On Thu, 31 Oct 2002, Tamas E. Gunda wrote: > Hi, > > Do you actually mean pyramidality, don't? The out-of-plane displacement > is not the best measure, as it depends on the bond lengths. > For different possibilities (such as POAV or P index) > have a look at > http://www.compuchem.com/m2m2.htm > > > Tamas > > Dr. Tamas E. Gunda > University of Debrecen, > H-4010 Debrecen, Hungary > tamasgunda@tigris.klte.hu > > ----- Original Message ----- > From: "Peter Gannett" > To: > Sent: Wednesday, October 30, 2002 22:49 > Subject: CCL:calculate tau (out of plane displacement) > > > > Hi > > > > I'm trying to calculate tau, the out of plane displacement for a > > central atom to which three others are attached (eg for I-J-K-L, K is > > the central atom, I, J, L are attached), assuming you know all bond > > lengths between K and the attached atoms and all angles (I-K-L, etc). I > > have made a weak attempt at coming up with this but since this value is > > often reported (without reference as to how it was determined/calc) I > > was hoping that someone had the necessary equations to figure this out. > > Thanks. > > > > Pete > > > > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins > > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: > jkl@ccl.net > > > > > > > > > > > > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > Dr. Harald Svedung cellphone: +49-175 736 2576 Institut f黵 Physikalische Chemie or: +46-709-223 206 Universit鋞 Karlsruhe Fritz-Haber-Weg 4 D-761 28 Karlsruhe Tyskland Tel: +49-721 608 2715 Fax:+49-721 608 6524 From chemistry-request@server.ccl.net Thu Oct 31 00:10:18 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9V5AIf14023 for ; Thu, 31 Oct 2002 00:10:18 -0500 Received: from cornell.edu (cs666981-224.satx.rr.com [66.69.81.224]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id AAA05780; Thu, 31 Oct 2002 00:10:17 -0500 (EST) Message-ID: <3DC0BB35.CEB94F25@cornell.edu> Date: Wed, 30 Oct 2002 23:10:13 -0600 From: "Dr. Richard L. Wood" Organization: Cornell University X-Mailer: Mozilla 4.5 [en]C-CCK-MCD {TLC;RETAIL} (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Gaussian questions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I've moved on from CHARMm and I'm just beginning with Gaussian and I am having some difficulties. I'm trying to find the transition state in a reaction, but it won't seem to do what I want it to (It could be that I'm not using the correct commands). Here's part of my input file: $RunGauss %chk=test2.chk #opt=(calcall,ts) freq=noraman rb3lyp/6-31g test2 -1 1 I know that some of my commands are not correct. I also want to use a different basis set than a 6-31g. What I have runs, but it gives me 21 imaginary frequencies and it stops, giving me the following message: Error termination request processed by link 9999. Error termination via Lnk1e in /usr/gaussian/g98/l9999.exe. I also tried to increase the number of cycles N to 1000 by using MaxCyc=1000, but the program tells me that N=104. I would appreciate any help anyone can offer. -- Richard L. Wood, Ph. D. Physical/Computational Chemist From chemistry-request@server.ccl.net Thu Oct 31 01:53:10 2002 Received: from mum.mans.edu.eg ([193.227.50.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9V6r8f16322 for ; Thu, 31 Oct 2002 01:53:09 -0500 Received: by mum.mans.edu.eg with Internet Mail Service (5.5.2656.59) id ; Thu, 31 Oct 2002 08:56:54 +0200 Message-ID: <4C7A402190F4BD4385075D6B739AB4141394FC@mum.mans.edu.eg> From: Tarek Mamoun El-Gogary To: "'CHEMISTRY@ccl.net'" Subject: summary: solvent cutoff wavelength Date: Thu, 31 Oct 2002 08:56:53 +0200 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2656.59) Content-Type: text/plain; charset="iso-8859-6" Dear CCLer's: Here is the replies to my question: Dear CCL members, > I am sorry to post this general question. > I am using a double beam spectrophotometer to measure the electronic > absorption spectra of some organic compounds, so I am using the solvent as a > blank and run autozeroing before scanning the sample. My question is: should > I stop scanning at the cutoff wavelength (240 nm) of the solvent or may I > measure the samble beyond the cutoff wavelength of the solvent? As the > solvent is in the blank cell so its interference will be eliminated, is that > correct? > regards > Tarek ---------------------------------------------------------------- ---------------------------------------------------------------- REPLIES: Dear Tarek, Well, if you ran autozeroing with the same solvent in both cells and use that information in running the sample against the solvent, you are perfectly OK. One of your test should proabbly be in the autozeroing step, where you should get either a rising line or a descending one as you gather the spectrum from longer to shorter wavelength. The reason is of course that the all solvents have very large peaks in the sigma-sigma* region which is under 200nm and even a tiny difference between the cells, of 0.001cm will give rise to large absorption differences - you have a hign molarity of your solvent (~55 for water so A= eps*l*c can get fairly large). I hope that this helps, Amiram ================================================= Dear Tarek, There is usually no need to stop scanning at the cutoff point. However, any results below that point should be treated with caution. It is possible that you could get spurious peaks in that region; this depends on what particular type of spectrophotometer you are using. The older machines with mechanical chopper mechanisms were very prone to this type of artifact. Modern ratio recording machines are a lot less prone to this effect Remember also that the cutoff is not necessarily a sharp point. My advice would be to check the actual absorption of the solvent by running a spectrum of the solvent (+ cell) against air. Remember also that you will be able to work at lower wavelengths if you use a thin cell (1 mm) rather than the usual size (10 mm). Also read what the manufacturer's manual says about the sensitivity at low transmissions. Cheers Peter Bladon =========================================================== Hi, It is also useful to measure the solvent and the sample separately and extract the solvent spectrum from that of the sample. It can be done by most of theavailable spectrophotometers with a built-in function. Best, Csaba ============================================================ Dear Tarek, If the solvent does not transmit light below 240 nm, then any data collected in that solvent would be meaningless. If some small amount of light is transmitted (the most likely case) then you will obtain some data below 240 nm, but the noise will be greatly increased. You could check the definition of 'cutoff wavelength' to see whether it means 0.1%, 1% or 10% of full intensity, etc. Generally, data collected below the solvent cutoff would be considered unreliable. Regards, Steve ========================================================= Dear Tarek: My experience with this kind of problem suggests that you can't go much below the cutoff wavelength for the solvent, even if you are using it as blank in a double beam instrument. The problem is that as you get beyond the cutoff wavelength, you still aren't going to get enough light through the blank to allow for a really proper correction. Most instruments will try to take things as far as you can, but sooner or later you get so little signal through the blank that the instrument has a hard time trying to apply any blank correction because the signal is so weak and noisy. So, you might be able to push it a bit, but really not too far. Hope this was of some help. Brian Williams,Chemistry Buckenll University ============================================ I take it you are using UV-Vis. Generally, one doesn't scan beyond the cutoffs of the equipment, whether this is the cufoff of the optics, the glassware (quartz in your case, I suspect, but Pyrex will do for > 290 or so), or the solvent. Even well matched cells will have some differential absorption for the solvent in this situation. A good peak deconvolution program might recover some sample information in this region -- this may be a function of software provided with modern spectrometers, but not with older dual-beam instruments. You should consult the manufacturer's literature, or some of the standard texts on care and feeding of UV measurements. Cheers, Steve ================================================ Tarek The problem with measuring the absorbance in a region where the solvent absorbs is that very little light makes it to the instrument's detector, even for the blank. Thus you would be trying to detect the difference between the very low light intensity for your reference and an even lower intensity for the sample plus solvent. In practice, most instruments allow enough stray light to reach the detector to make the measurement you're describing suspect at best. Therefore, the solvent blank does not assure a meaningful result, and subtracting the spectrum of the solvent > from the spectrum of the solution is not likely to help. Adherence to Beer's law (the linearity of absorbance with concentration) would perhaps suggest that your results are meaningful. ciao, Bruce Bruce Palfey Department of Biological Chemistry University of Michigan Ann Arbor, MI 48109-0606 *END* ================================ From chemistry-request@server.ccl.net Wed Oct 30 21:47:50 2002 Received: from smtp01.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9V2lkf09900 for ; Wed, 30 Oct 2002 21:47:47 -0500 Received: from PC12 (unknown [202.127.19.236]) by smtp01.sohu.com (Postfix) with ESMTP id 96E2553762 for ; Thu, 31 Oct 2002 10:23:17 +0800 (CST) Date: Thu, 31 Oct 2002 10:49:34 +0800 From: "zgleo" To: "CHEMISTRY@ccl.net" Subject: Autodock question X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon061867741472_=====" Message-Id: <20021031022317.96E2553762@smtp01.sohu.com> This is a multi-part message in MIME format. --=====000_Dragon061867741472_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: quoted-printable Dear CCLer, =09I'm using autodock3.0 and encouter such prompt information when= making autogrid: =09 =09"WARNING!Attempt to divide by zero was just prevented. =09Are the coordinates of atoms 2194 and 2681 the same?" =09 =09Why comes out such prompt?What should I response to it,yes or= no? =09Eager to know the answer,thanks. =09=09=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1zgleo =A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1zgliu@sohu.com =A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A1=A12002-10-31 --=====000_Dragon061867741472_===== Content-Type: image/gif; name="fox.gif" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="fox.gif" R0lGODlhIwAfALMLAP///+Dg4OCgAOCAAOAAAMDA4KCgwKBgQIAAAGBggCAgIAAAAAAAAAAAAAAA AAAAACH/C05FVFNDQVBFMi4wAwHoAwAh+QQJDwALACwAAAAAIwAfAAAE+3DJSem5Na+jux3CxWWi Zx5DIgiD6Lrgan6FoYZDzuborKGDQKEAXBl1Al/lEgwUjcaeTClhBpDQ6ECypYqwzauAuOhSN8BY 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187FFH-0005De-02 for chemistry@ccl.net; Thu, 31 Oct 2002 13:20:23 +0000 Received: from hbtower.ch.ic.ac.uk ([155.198.226.132] helo=ic.ac.uk) by chcmga.ch.ic.ac.uk with esmtp (Exim 3.36 #1) id 187FHP-006TWI-00 for chemistry@ccl.net; Thu, 31 Oct 2002 13:22:35 +0000 Sender: krzys@mr2.cc.ic.ac.uk Message-ID: <3DC12D94.6D2CB9AA@ic.ac.uk> Date: Thu, 31 Oct 2002 13:18:12 +0000 From: Krzysztof Radacki Organization: Imperial College, London X-Mailer: Mozilla 4.78 [en] (X11; U; Linux 2.4.7-10smp i686) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: tyan boards Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, I use dual-proccessor tyan mainboards (S2462) for g98 and generaly I'm quite happy with them. Unfortuantely I've found that if difference of temperature between both proccessores is larger then 4-5 degree system becomes unstable. Is somebody aware of software runing under linux wich can report temperature from hardware sensors of board? With kind regards K.Radacki p.s. Tyan has written me that they have no support for linux. -- Dr. K.Radacki Department of Chemistry Catalysis and Advanced Materials Section Imperial College, London From chemistry-request@server.ccl.net Thu Oct 31 09:06:10 2002 Received: from fyserv1.fy.chalmers.se ([129.16.110.66]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VE69f28000 for ; Thu, 31 Oct 2002 09:06:10 -0500 Received: from fy.chalmers.se (ftf-pc32.fy.chalmers.se [129.16.112.162]) by fyserv1.fy.chalmers.se (8.8.8/8.8.8) with ESMTP id PAA18012; Thu, 31 Oct 2002 15:06:01 +0100 (MET) Message-ID: <3DC13944.F7D73910@fy.chalmers.se> Date: Thu, 31 Oct 2002 15:08:04 +0100 From: Patrik Johansson Organization: CTH X-Mailer: Mozilla 4.51 [sv] (Win98; I) X-Accept-Language: sv MIME-Version: 1.0 To: Patrik Johansson , chemistry@ccl.net Subject: Summary:Once again: units in gaussian References: <3DB9048F.B3A30E6B@fy.chalmers.se> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Several people pointed out to me that I could do a calc and then compare with tables - but more assuring I got response from Doug Fox that stated that the units are au. A big thank you to everyone who responded. /Patrik Original question below. Patrik Johansson skrev: > > Hi CCLers > > I have seen this Q in the archives (many times) - but no answer: > > What are the units used by G98 for polarisabilities and > hyperpolarisabilities? I.e. are they a.u.**3 or Angstrom**3 ? > > I've sent the same Q to Gaussian - and if I get response I will post it > to the list. > > regards > > /Patrik > -- > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Patrik Johansson (patrikj@fy.chalmers.se) Scientist @ Materials Physics Group Chalmers University of Technology 412 96 Goteborg SWEDEN NEW!!! http://fy.chalmers.se/mf/Computer.html http://fy.chalmers.se/~jpatrik/ From chemistry-request@server.ccl.net Thu Oct 31 09:10:10 2002 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VEAAf28151 for ; Thu, 31 Oct 2002 09:10:10 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 187FxG-0002wz-00; Thu, 31 Oct 2002 14:05:50 +0000 Date: Thu, 31 Oct 2002 14:05:50 +0000 (GMT) From: Szilveszter Juhos To: Krzysztof Radacki cc: CCL Subject: Re: CCL:tyan boards In-Reply-To: <3DC12D94.6D2CB9AA@ic.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Thu, 31 Oct 2002, Krzysztof Radacki wrote: > I use dual-proccessor tyan mainboards (S2462) for check: http://secure.netroedge.com/~lm78/index.html It should work, yes. Szilva From chemistry-request@server.ccl.net Thu Oct 31 10:24:11 2002 Received: from travelers.mail.cornell.edu ([132.236.56.13]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VFOBf29771 for ; Thu, 31 Oct 2002 10:24:11 -0500 Received: from travelers.mail.cornell.edu (travelers.mail.cornell.edu [132.236.56.13]) by travelers.mail.cornell.edu (8.9.3/8.9.3) with SMTP id KAA03461; Thu, 31 Oct 2002 10:24:07 -0500 (EST) Date: Thu, 31 Oct 2002 10:24:07 -0500 (EST) From: jdg9@cornell.edu X-Sender: jdg9@travelers.mail.cornell.edu To: Krzysztof Radacki cc: CCL Subject: Re: CCL:tyan boards In-Reply-To: <3DC12D94.6D2CB9AA@ic.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII For temperature monitoring under Linux, check out the lm_sensors package (http://www2.lm-sensors.nu/~lm78/). You'll need to verify that your particular hardware is supported. Regards, Jason Gans On Thu, 31 Oct 2002, Krzysztof Radacki wrote: [...] > Is somebody aware of software runing under linux > wich can report temperature from hardware sensors > of board? > From chemistry-request@server.ccl.net Thu Oct 31 14:29:50 2002 Received: from anes-nt02.anes.upmc.edu ([128.147.32.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VJTof03538 for ; Thu, 31 Oct 2002 14:29:50 -0500 Received: by anes-nt02.anes.upmc.edu with Internet Mail Service (5.5.2653.19) id ; Thu, 31 Oct 2002 14:29:50 -0500 Message-ID: <5DE64C592075AD4EBEE86F6AB65F8C6501923857@anes-nt02.anes.upmc.edu> From: "Liu, Zhanwu" To: "'chemistry@ccl.net'" Subject: Help for Gaussian98 compilation Date: Thu, 31 Oct 2002 14:29:50 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain Hi, I was trying to compile Gaussian 98 on the Linux using pgf77 trial), at first it always report "pthreads_creat not ...", then I modified the g98.make file to link libpthread.so.0 into util.so; then compilation could continue on until l402.exe, the compiler reported "multiple defination" of a series of functions, and stopped. The linux distribution is Redhat 7.3 preloaded on Dell workstation. Have anyone encountered the same problem? Thanks! Zhanwu Liu ---------------------- Zhanwu Liu, Ph.D. Department of Anesthesiology University of Pittsburgh From chemistry-request@server.ccl.net Thu Oct 31 12:02:34 2002 Received: from anor.ics.muni.cz ([147.251.4.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VH2Xf32336 for ; Thu, 31 Oct 2002 12:02:34 -0500 Received: from bilbo.chemi.muni.cz (bilbo.chemi.muni.cz [147.251.28.2]) by anor.ics.muni.cz (8.12.1/8.12.1) with ESMTP id g9VH2SQV010778 for ; Thu, 31 Oct 2002 18:02:28 +0100 Received: from ncbr.chemi.muni.cz (ncbr.chemi.muni.cz [147.251.28.55]) by bilbo.chemi.muni.cz (8.9.3/8.8.5) with ESMTP id SAA14533 for ; Thu, 31 Oct 2002 18:02:28 +0100 (MET) Received: from ncbr.chemi.muni.cz (ncbr.chemi.muni.cz [147.251.28.55]) by ncbr.chemi.muni.cz (8.11.3nb1/8.10.1) with ESMTP id g9VH2SJ09504 for ; Thu, 31 Oct 2002 18:02:28 +0100 (MET) Date: Thu, 31 Oct 2002 18:02:28 +0100 (MET) From: Jana Precechtelova To: "CCL.NET" Subject: freezing heavy atoms, unfreezing hydrogens Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Muni-Virus-Test: Clean I`d like to perform a geometry optimization (in Gaussian) of a molecule defined by cartesian coordinates. During the optimization, I need to freeze heavy atoms but let hydrogens to be optimized. How can I easily achieve this? I`ve already tried it using a ModRedundant option to the Opt keyword and by specifying atoms to be fixed via this sequence: X N F (N is a number of atom) but this attempt failed. Best regards, Jana Precechtelova -------------------------------------------------------------------------- Jana Precechtelova National Centre for Biomolecular Research (NCBR) Faculty of Science Masaryk University Kotlarska 2 email: janap@ncbr.chemi.muni.cz 611 37 Brno phone: +420-5-41129588 The Czech Republic fax: +420-5-411 29 506 -------------------------------------------------------------------------- From chemistry-request@server.ccl.net Thu Oct 31 08:11:42 2002 Received: from mailhub.health.nb.ca ([207.179.181.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VDBgf26965 for ; Thu, 31 Oct 2002 08:11:42 -0500 Received: from health.nb.ca ([10.10.94.100]) by mailhub.health.nb.ca (Post.Office MTA v3.5.3 release 223 ID# 607-58282U90000L90000S0V35) with ESMTP id ca for ; Thu, 31 Oct 2002 09:11:38 -0400 Message-ID: <3DC12B72.7090705@health.nb.ca> Date: Thu, 31 Oct 2002 09:09:06 -0400 From: miroslavac@health.nb.ca (Miroslava Cuperlovic-Culf) User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:0.9.2.1) Gecko/20010901 X-Accept-Language: en-us MIME-Version: 1.0 To: ccl Subject: Glycosylation & Phosphorylation Content-Type: multipart/alternative; boundary="------------010303050000010602090201" --------------010303050000010602090201 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Dear All, I would like to find out more about theoretical methods for studying glycosilation and phosphorylation of proteins. Are there any programs (ideally free) for prediction, modelling of it. Also any references would be appreciated. Thanks for the ongoing help, Cheers, Mira -- Miroslava Cuperlovic-Culf, Ph.D. Research Scientist Beausejour Medical Research Institute (IRMB) Dr. Leon Richard Oncology Center 37 Providence Street Moncton, NB E1C 8X3 Canada fax: 506-862-4222 tel: 506-862-4848 e-mail: miroslavac@health.nb.ca --------------010303050000010602090201 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit Dear All,
I would like to find out more about theoretical methods for studying glycosilation and phosphorylation of proteins. Are there any programs (ideally free) for prediction, modelling of it.
Also any references would be appreciated.
Thanks for the ongoing help,
Cheers,
Mira

--
mail_signature Miroslava Cuperlovic-Culf, Ph.D.
Research Scientist
Beausejour Medical Research Institute (IRMB)
Dr. Leon Richard Oncology Center
37 Providence Street
Moncton, NB E1C 8X3
Canada
fax: 506-862-4222
tel: 506-862-4848
e-mail: miroslavac@health.nb.ca
--------------010303050000010602090201-- From chemistry-request@server.ccl.net Thu Oct 31 09:18:13 2002 Received: from atom.ecn.purdue.edu ([128.46.108.94]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VEIDf28407 for ; Thu, 31 Oct 2002 09:18:13 -0500 Received: from ecn.purdue.edu (chme117bpc3.ecn.purdue.edu [128.46.108.125]) (authenticated bits=0) by atom.ecn.purdue.edu (8.12.5/8.12.5) with ESMTP id g9VEI707000037; Thu, 31 Oct 2002 09:18:08 -0500 (EST) Message-ID: <3DC13B9F.BE093EC8@ecn.purdue.edu> Date: Thu, 31 Oct 2002 09:18:07 -0500 From: Aaron Deskins Organization: Purdue University X-Mailer: Mozilla 4.79 [en] (Windows NT 5.0; U) X-Accept-Language: en MIME-Version: 1.0 To: Richard Gillilan CC: CCL Subject: Re: CCL:damped molecular dynamics References: <3DBEE809.F4D7E0C5@ecn.purdue.edu> <3DBFE842.B4D8D62@cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned-ECN: by AMaVIS version 11 (http://amavis.org/) Thank you for your reply. I should have mentioned in my original email that I'm working with a solid state system, specifically modelling of surfaces. I have access to programs that implement tight-binding and DFT methods. I have had some good results, but still need to work on my simulations. My main area of confusion concerns what to do when the kinetic energy has been damped to essentially zero, but I am not yet at the potential energy minimum. thank you. Richard Gillilan wrote: > > In dynamics with friction and stochastic terms there is the > tendency to mask problems in the underlying trajectory > integration/dynamics. I believe the step size should be > chosen so that zero-friction dynamics is stable for long > time ... that way you know the underlying dynamics is good. > Usually for dynamics, you would choose a stepsize of 1 or 2 > fsec when hydrogen atoms are present. With a unified atom model > or bond-length constraints you can go larger. The step size you > need must be smaller than a typical oscillation period for any > coordinate. Oscillation period depends upon both the stiffness > of the spring and the effective mass of the atom or body. > > You could then turn up the friction a little to give you > what you want. I assume you are using it as a sort of > simulated annealing? > > I would love to know how others choose good friction terms for > Langevin type simulations. Perhaps others will comment. > > Richard Gillilan > MacCHESS, Cornell > > > 2) What are good strategies to decide the friction coefficient and time > > step? I noticed that if the time step is too large, the kinetic > > instabilities are common. > > > > thanks for any help. > > > > Aaron Deskins > > Purdue University > > > From chemistry-request@server.ccl.net Thu Oct 31 18:13:09 2002 Received: from mail500.nifty.com ([202.248.37.208]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9VND8f13141 for ; Thu, 31 Oct 2002 18:13:09 -0500 Received: from TP-R32.mb.infoweb.ne.jp by mail500.nifty.com (8.12.6/3.7W-07/15/02) with ESMTP id g9VNBsut002152; Fri, 1 Nov 2002 08:11:56 +0900 Message-Id: <5.0.2.7.2.20021101081136.050ea138@pop.nifty.com> X-Sender: fwip5390@pop.nifty.com X-Mailer: QUALCOMM Windows Eudora Version 5.0.2-Jr2 Date: Fri, 01 Nov 2002 08:11:46 +0900 To: "Liu, Zhanwu" , "'chemistry@ccl.net'" From: Aaron Goto Subject: Re: CCL:Help for Gaussian98 compilation In-Reply-To: <5DE64C592075AD4EBEE86F6AB65F8C6501923857@anes-nt02.anes.up mc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Hi, This is known problem, and there is a fixed version on there web site. You can download fixed "libthreads.so" from following URL. ftp://ftp.pgroup.com/x86/linux86-patches/redhat73 Regards, Aaron At 14:29 02/10/31 -0500, Liu, Zhanwu wrote: >Hi, > >I was trying to compile Gaussian 98 on the Linux using pgf77 trial), at >first it always > report "pthreads_creat not ...", then I modified the g98.make file to >link libpthread.so.0 >into util.so; then compilation could continue on until l402.exe, the >compiler reported >"multiple defination" of a series of functions, and stopped. The linux >distribution is >Redhat 7.3 preloaded on Dell workstation. Have anyone encountered the >same problem? >Thanks! > >Zhanwu Liu >---------------------- >Zhanwu Liu, Ph.D. >Department of Anesthesiology >University of Pittsburgh > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net