From chemistry-request@server.ccl.net Thu May 16 02:46:32 2002 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4G6kV910597 for ; Thu, 16 May 2002 02:46:32 -0400 Received: from iris.sipp.ac.cn [202.127.18.184] by iris.sipp.ac.cn with ESMTP (SMTPD32-6.04) id A727156E0146; Thu, 16 May 2002 14:52:23 +0800 Sender: xmao@ccl.net Message-ID: <3CE205F8.E33AA169@iris.sipp.ac.cn> Date: Wed, 15 May 2002 14:53:45 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn X-Mailer: Mozilla 4.78C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: question about optimisation using QM Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit hello everyone: Here is a question about optimisation in GAMESS-US. When I ran a optimization on a molecule, first I optimize it using sto-3g, and then I calculate the frequency on the optimized molecule. I have read that if a molecule is in its mimimum, it must have 6 frequencies near zero. So I wonder if my calculation step is right. Today, when I optimize a molecule, it always tell me that it is not a stationary point(I have got three frequencies under 15cm-1, and three under 0.1 cm-1). So here is another question, I wonder what the size of the frequency that I could consider it as near zero. And does the warning from the program means that I should reoptimize my molecule. If so, how I could generate or modify the input molecule , because I always generate the coordinate using insightII. Thanks in advance. Best Regards, mao From chemistry-request@server.ccl.net Thu May 16 06:28:41 2002 Received: from yello.theochem.ruhr-uni-bochum.de (IDENT:root@[134.147.125.174]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GASe916827 for ; Thu, 16 May 2002 06:28:40 -0400 Received: from yello.theochem.ruhr-uni-bochum.de (akohlmey@localhost) by yello.theochem.ruhr-uni-bochum.de (8.11.6/8.11.0) with ESMTP id g4GASWV02182; Thu, 16 May 2002 12:28:32 +0200 Message-Id: <200205161028.g4GASWV02182@yello.theochem.ruhr-uni-bochum.de> X-Authentication-Warning: yello.theochem.ruhr-uni-bochum.de: akohlmey owned process doing -bs From: axel.kohlmeyer@theochem.ruhr-uni-bochum.de To: weiz@mail.rochester.edu, cpmd-list@cpmd.org cc: CHEMISTRY@ccl.net, akohlmey@yello.theochem.ruhr-uni-bochum.de Subject: Re: [CPMD-list] help on parellel computing In-reply-to: Your message of "Wed, 15 May 2002 13:13:11 EDT." <200205151711.g4FHBTsT14989221@mail.rochester.edu> Reply-To: axel.kohlmeyer@theochem.ruhr-uni-bochum.de User-Agent: EMH/1.10.0 SEMI/1.13.7 (Awazu) CLIME/1.13.6 (=?ISO-2022-JP?B?GyRCQ2YlTj4xGyhC?=) MULE XEmacs/21.1 (patch 14) (Cuyahoga Valley) (i386-redhat-linux) MIME-Version: 1.0 (generated by SEMI 1.13.7 - "Awazu") Content-Type: text/plain; charset=US-ASCII Date: Thu, 16 May 2002 12:28:32 +0200 >>> "WZ" == weiz writes: WZ> Hi, friends: WZ> I was running CPMD program on a linux cluster, I set the restart file to be WZ> saved every 5 steps. however, every time when the machine is going to save WZ> the restart file. the job is crashed. and following is the information. could WZ> anybody give me some clue about what is wrong here and any suggestion of how WZ> to solve it. thanks a lot. WZ> wei zhuang WZ> ----------------- WZ> MPI_Recv: process in local group is dead (rank 4, MPI_COMM_WORLD) WZ> MPI_Recv: process in local group is dead (rank 1, MPI_COMM_WORLD) WZ> MPI_Recv: process in local group is dead (rank 8, MPI_COMM_WORLD) WZ> MPI_Recv: process in local group is dead (rank 2, MPI_COMM_WORLD) hiho! it looks as if you have overloaded your network and the ethernet driver skipped a few packages (or the pci bus lost some interrupts). some combinations of pc hardware get severly overloaded if you run large parallel cpmd jobs, especially with TCP/IP networking. can you describe the kind of network (network cards, switch) and driver software (linux kernel, network driver) you are using. also it would be helpful to know, whether the same job runs single cpu and how 'large' the job, i.e. how big the restart file is. cheers, axel. -- ======================================================================= Axel Kohlmeyer e-mail: axel.kohlmeyer@theochem.ruhr-uni-bochum.de Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673 Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045 D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de ======================================================================= If you make something idiot-proof, the universe creates a better idiot. From chemistry-request@server.ccl.net Thu May 16 01:56:43 2002 Received: from carbon.chem.ucla.edu ([128.97.35.55]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4G5uh909073 for ; Thu, 16 May 2002 01:56:43 -0400 Received: from [128.97.147.217] (ch-17.psnet.ucla.edu [128.97.147.217]) by carbon.chem.ucla.edu (8.11.4/8.11.4) with ESMTP id g4G5uTh25312; Wed, 15 May 2002 22:56:29 -0700 (PDT) Mime-Version: 1.0 Message-Id: In-Reply-To: References: Date: Fri, 1 Jan 1904 21:44:08 -0800 To: Roy Jensen From: Eric Scerri Subject: Re: CCL:Hybridization... Cc: ccl Content-Type: text/plain; charset="us-ascii" ; format="flowed" I assume you have tried the obvious? A search of the excellent Journal of Chemical Education on-line Index at http://jchemed.chem.wisc.edu/Journal/Search/index.html Please let me know if you find any good discussions on hybridization in this or other journals. Each time I teach it I resolve to try to clear up my priorities on this topic and to get the philosophical picture clear but have never got round to it yet. regards, eric scerri >Students leave first-year chemistry with the belief that hybridization is >the gospel wrt bonding. So much so that bonding in diatomics, HCl, Cl2, >etc., is sometimes taught as occuring through hybridized orbitals: >experiment, symmetry, and ab-initio calcs indicate otherwise. > >Is there an article that discusses this at the non-specialist (graduate/ >undergraduate) level? I vaguely recall a website that details this for >HCl. Can anyone point me to the website again? > >Roy Jensen > >I will summarize to the List. > > >-= 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 -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri@chem.ucla.edu tel: 310 206 7443 fax: 310 206 2061 Web Page: http://www.chem.ucla.edu/dept/Faculty/scerri/index.html Editor of Foundations of Chemistry http://www.kluweronline.com/issn/1386-4238 Also see International Society for the Philosophy of Chemistry http://www.georgetown.edu/earleyj/ISPC.html From chemistry-request@server.ccl.net Thu May 16 06:33:26 2002 Received: from relay.unizar.es ([155.210.3.20]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GAXO916994 for ; Thu, 16 May 2002 06:33:24 -0400 Received: from celes.unizar.es (celes.unizar.es [155.210.11.15]) by relay.unizar.es (8.11.1/8.11.1) with ESMTP id g4GAX8524566; Thu, 16 May 2002 12:33:08 +0200 (MET DST) Received: from there (santiago@[155.210.93.83]) by celes.unizar.es (8.11.1/8.11.1) with SMTP id g4GAVwT16087; Thu, 16 May 2002 12:31:58 +0200 (MET DST) Message-Id: <200205161031.g4GAVwT16087@celes.unizar.es> Content-Type: text/plain; charset="iso-8859-1" From: Santiago Cuesta <405137@docto.unizar.es> Reply-To: 405137@docto.unizar.es Organization: Ciencias To: rlw28@cornell.edu Subject: CCL: summary hbonds charmm (thanks) Date: Thu, 16 May 2002 12:32:16 +0200 X-Mailer: KMail [version 1.3.2] References: <200205151223.g4FCNWT14221@celes.unizar.es> <3CE25BB8.3A620001@cornell.edu> In-Reply-To: <3CE25BB8.3A620001@cornell.edu> Cc: chemistry@ccl.net, rvenable@gandalf.cber.nih.gov MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Hi !! I want to thank Dr Richard L. Wood and Mr Rick Venable their help. Thanks very much for solving my problem !! . Thanks also to CCL ! Yours sincerely Santiago Now the summary: ---------------------------------------------- how to calculate time series with charmm (academic version) dihedrals and hbonds???: --------------------------------------------------------- On Wed, 15 May 2002, Santiago Cuesta wrote: > I'm trying to calculate hbonds time correlation series from  MD trayectories > with the academic version of charmm. >  > After reading correctly trayectories, I've used: >  >  correl maxseries 12 maxtimesteps 50000 maxatom 80 - >   eps 1.0  cutnb @4 ctofnb @6 ctonnb @5 vswi - >   ewald pmewald kappa @kap fftx 32 ffty 32 fftz 32 order @ord - >   @7 @8 @9 - >   inbf 1 ihbf 1 imgf 1 >  >  enter phi1 dihe prot 24 C prot 25 N  prot 25 CA  prot 25 C geometry >  enter psi1 dihe prot 25 N prot 25 CA  prot 25 C  prot 26 N geometry >  enter phi2 dihe prot 28 C  prot 29 N  prot 29 CA  prot 29 C geometry >  enter psi2 dihe prot 29 N  prot 29 CA  prot 29 C  prot 30 N geometry >  >  enter phi1 time >  enter psi1 time >  enter phi2 time >  enter psi2 time >  > ! (HBONDS) >  >  enter hbn1 hbond  prot 31 N  prot 16 OE2  DIST > ! or ( enter hbn1 hbond prot 31 N prot 31 HN prot 16 OE2  DIST >  enter hbn1 time >  >  > BUT I obtain this error: >  >  > : No hydrogen bond parameters for     1 ( NH1  OH1 ) >  ------------------------------------ ANSWERS: ------------ > From Dr Richard L. Wood: *************** Hi Santiago You need to read in h-bond parameters from a file, something like this: OPEN READ CARD UNIT 3 NAME "par_hbond.inp" READ PARAM APPEND CARD UNIT 3 CLOSE UNIT 3 where par_hbond.inp is a file that has the parameters for hydrogen bonds. You will also need to make sure that your residue topology file has all the correct donors and acceptor atoms defined. Hope this helps... Richard **************** > From Rick Venable: --------------------- For the academic parameters, the H-bond parameters are in a separate file, largely because they are unused except for analysis.  Add the following after reading your parameter file: open read unit 2 card name @PATH/par_hbond.inp read param unit 2 append close unit 2 where @PATH is the full or relative pathname to the appropriate 'toppar' subdir. ************************************ ------------------------------------- Santiago Cuesta Predoctoral student Dep. Física de la Materia Condensada. Universidad de Zaragoza. (Spain) > > > > -= 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 Thu May 16 03:32:05 2002 Received: from bohr.quantchem.kuleuven.ac.be ([134.58.49.6]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4G7W4912975 for ; Thu, 16 May 2002 03:32:05 -0400 Received: (qmail 14937 invoked by uid 245); 16 May 2002 07:32:19 -0000 Date: Thu, 16 May 2002 09:32:19 +0200 (CEST) From: Liviu Chibotaru X-Sender: liviu@localhost.localdomain To: chemistry@ccl.net cc: jkl@ccl.net Subject: XVI Jahn-Teller Conference Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Please visit the site of the XVI-th Jahn-Teller Conference http://www.chem.kuleuven.ac.be/jahn-teller/ -- ============================================================================== = Liviu Chibotaru = = Lab of QuantumChemistry Tel:(32)(16)327476 = = University of Leuven Fax:(32)(16)327992 = = Celestijnenlaan 200F / B-3001 Heverlee / Belgium = = E-mail: Liviu.Chibotaru@chem.kuleuven.ac.be ============================================================================== From chemistry-request@server.ccl.net Thu May 16 10:51:17 2002 Received: from web15004.mail.bjs.yahoo.com ([61.135.128.7]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4GEpGk23170 for ; Thu, 16 May 2002 10:51:16 -0400 Message-ID: <20020516145109.76038.qmail@web15004.mail.bjs.yahoo.com> Received: from [202.99.57.126] by web15004.mail.bjs.yahoo.com via HTTP; Thu, 16 May 2002 22:51:09 CST Date: Thu, 16 May 2002 22:51:09 +0800 (CST) From: =?gb2312?q?yong=20pei?= Subject: Can dynamics pressure of the MD simulation compared with surface tension? To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 8bit Dear Sir I want to know the relation between the dynamics pressure and the surface tension of liquid . Regards, Y Pei P.R.China _________________________________________________________ Do You Yahoo!? ̯¿ªÄãµÄÕÆÐÄ ÈÃÎÒ¿´¿´Äã http://sweepstakes.yahoo.com/2002cnuser From chemistry-request@server.ccl.net Thu May 16 10:42:42 2002 Received: from f04n07.cac.psu.edu ([128.118.141.35]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GEggk22966 for ; Thu, 16 May 2002 10:42:42 -0400 Received: from ra.chem.psu.edu (ra.chem.psu.edu [128.118.199.40]) by f04n07.cac.psu.edu (8.9.3/8.9.3) with ESMTP id KAA78860 for ; Thu, 16 May 2002 10:42:42 -0400 Content-Type: text/plain; charset="us-ascii" From: Rajarshi Guha Reply-To: rajarshi@presidency.com To: CHEMISTRY@ccl.net Subject: searching for chemical structures Date: Thu, 16 May 2002 10:41:18 -0400 X-Mailer: KMail [version 1.4] MIME-Version: 1.0 Content-Transfer-Encoding: 8bit Message-Id: <200205161041.28154.rajarshi@presidency.com> -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, does anybody know of any free services where I can search for a molecule structure by name - apart form www.chemfinder.com? TIA, - -- - ------------------------------------------------------------------- Rajarshi Guha | email: rajarshi@presidency.com 417 Davey Laboratory | web : http:// www.jijo.cjb.net Dept. Of Chemistry | ICQ : 123242928 Pennsylvania State University | AIM : LoverOfPanda - ------------------------------------------------------------------- GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A Public Key : http://pgp.mit.edu/ - ------------------------------------------------------------------- All science is either physics or stamp collecting. -- Ernest Rutherford -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE848UXzcRVdJAXryoRAoJ6AKCxou1sKg4QYACyqJvC47OYHxpxQACgyxRZ t7P2yoexQ6SmJoVQjokEYNM= =5xkd -----END PGP SIGNATURE----- From chemistry-request@server.ccl.net Thu May 16 10:37:06 2002 Received: from lua.ifi.unicamp.br ([143.106.6.13]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GEb4k22870 for ; Thu, 16 May 2002 10:37:05 -0400 Received: by lua.ifi.unicamp.br (Postfix, from userid 106) id 8F150A9AA; Thu, 16 May 2002 11:36:55 -0300 (BRT) Received: from posdyn11.ifi.unicamp.br (posdyn11.ifi.unicamp.br [143.106.128.205]) by lua.ifi.unicamp.br (Postfix) with ESMTP id 85C7054F8 for ; Thu, 16 May 2002 11:36:54 -0300 (BRT) Message-Id: <5.1.0.14.0.20020516113508.00b1ca30@lua.ifi.unicamp.br> X-Sender: dasf@lua.ifi.unicamp.br X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Thu, 16 May 2002 11:39:39 -0700 To: CHEMISTRY@ccl.net From: "Demetrio A. da Silva Filho" Subject: Dipole in G98 output Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_70948796==_.ALT" X-AntiVirus: scanned for viruses by AMaViS 0.2.1 (http://amavis.org/) --=====================_70948796==_.ALT Content-Type: text/plain; charset="us-ascii"; format=flowed Dear CCL'ers, In Gaussian'98 output, there is a section where it displays the Dipole moment, for example: Dipole moment (Debye): X= 0.2383 Y= 0.0000 Z= -0.1582 Tot= 0.2861 But then, at the very last lines, I can find: 5683381671,0.2110329447,-2.3001060907\\Version=SGI64-G98RevA.7\HF=-162 7.8627523\RMSD=6.034e-09\RMSF=5.127e-06\Dipole=6.366688,-0.3919573,0.0 736125\PG=C01 [X(C22H14S2)]\\@ What kind of Dipole is this? Thanks in advance, Demetrio Filho ________________________ "Success comes in cans, failure in can'ts." - Unknown To know more about Zoa v2.0, visit its web site at http://zoa.freeservers.com --=====================_70948796==_.ALT Content-Type: text/html; charset="us-ascii" Dear CCL'ers,

In Gaussian'98 output, there is a section where it displays the Dipole moment, for example:

 Dipole moment (Debye):
    X=     0.2383    Y=     0.0000    Z=    -0.1582  Tot=     0.2861


But then, at the very last lines, I can find:

 5683381671,0.2110329447,-2.3001060907\\Version=SGI64-G98RevA.7\HF=-162
 7.8627523\RMSD=6.034e-09\RMSF=5.127e-06\Dipole=6.366688,-0.3919573,0.0
 736125\PG=C01 [X(C22H14S2)]\\@


What kind of Dipole is this?

Thanks in advance,

Demetrio Filho





________________________
"Success comes in cans, failure in can'ts."
- Unknown

To know more about Zoa v2.0, visit its web site at
http://zoa.freeservers.com
 --=====================_70948796==_.ALT-- From chemistry-request@server.ccl.net Thu May 16 11:37:46 2002 Received: from pcserver.iqm.unicamp.br ([143.106.51.10]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GFbkk24292 for ; Thu, 16 May 2002 11:37:46 -0400 Received: from localhost (localhost.iqm.unicamp.br [127.0.0.1]) by pcserver.iqm.unicamp.br (Postfix) with ESMTP id 563F33E1D for ; Thu, 16 May 2002 12:37:45 -0300 (BRT) Received: from iqm.unicamp.br (luxor.iqm.unicamp.br [143.106.51.146]) by pcserver.iqm.unicamp.br (Postfix) with ESMTP id 627D03E1A for ; Thu, 16 May 2002 12:37:43 -0300 (BRT) Message-ID: <3CE3D243.4070601@iqm.unicamp.br> Date: Thu, 16 May 2002 12:37:39 -0300 From: Milton Taidi Sonoda User-Agent: Mozilla/5.0 (X11; U; FreeBSD i386; en-US; rv:0.9.7) Gecko/20020123 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: .mol file Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by AMaViS perl-11 Hi all Does anybody know what molecular viewer for linux/unix/FreeBSD system that suports .mol extension? Thankx in advance Milton Taidi Sonoda From chemistry-request@server.ccl.net Thu May 16 11:57:20 2002 Received: from mhub2.bbsrc.ac.uk ([149.155.202.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GFvKk24969 for ; Thu, 16 May 2002 11:57:20 -0400 Received: from exrout.cc.bbsrc.ac.uk ([149.155.100.88]) by mhub2.bbsrc.ac.uk with esmtp (Exim 3.31 #1) id 178NaT-0001vH-04; Thu, 16 May 2002 16:54:41 +0100 Received: from bits-exch1.bits.bbsrc.ac.uk ([149.155.108.13]) by exrout.cc.bbsrc.ac.uk with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id LAL5QV6N; Thu, 16 May 2002 16:54:54 +0100 Received: by bits-exch1.bits.bbsrc.ac.uk with Internet Mail Service (5.5.2653.19) id ; Thu, 16 May 2002 16:54:54 +0100 Message-ID: <41773CEF2B8FD411920200508BDCDC12BE13FA@bits-exch1.bits.bbsrc.ac.uk> From: "michael hanlon (BITS)" To: "'Rajarshi Guha'" , CHEMISTRY@ccl.net Subject: RE: searching for chemical structures Date: Thu, 16 May 2002 16:54:53 +0100 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) Content-Type: text/plain; charset="iso-8859-1" X-ECS-MailScanner-BBSRC: Found to be clean These are popular: http://alpha2.bmc.uu.se/hicup/ http://triton.ps.toyaku.ac.jp/~dobashi/database/indexe.html Mike -----Original Message----- From: Rajarshi Guha [mailto:rajarshi@presidency.com] Sent: 16 May 2002 15:41 To: CHEMISTRY@ccl.net Subject: CCL:searching for chemical structures -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, does anybody know of any free services where I can search for a molecule structure by name - apart form www.chemfinder.com? TIA, - -- - ------------------------------------------------------------------- Rajarshi Guha | email: rajarshi@presidency.com 417 Davey Laboratory | web : http:// www.jijo.cjb.net Dept. Of Chemistry | ICQ : 123242928 Pennsylvania State University | AIM : LoverOfPanda - ------------------------------------------------------------------- GPG Fingerprint: DCCB 4D1A 5A8B 2F5A B5F6 1F9E CDC4 5574 9017 AF2A Public Key : http://pgp.mit.edu/ - ------------------------------------------------------------------- All science is either physics or stamp collecting. -- Ernest Rutherford -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE848UXzcRVdJAXryoRAoJ6AKCxou1sKg4QYACyqJvC47OYHxpxQACgyxRZ t7P2yoexQ6SmJoVQjokEYNM= =5xkd -----END PGP SIGNATURE----- -= 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 Thu May 16 15:09:00 2002 Received: from gordon.chem.wayne.edu (mer@[141.217.26.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4GJ90k29039 for ; Thu, 16 May 2002 15:09:00 -0400 Received: from localhost (mer@localhost) by gordon.chem.wayne.edu (8.10.2+Sun/8.10.2) with ESMTP id g4GJ8vp17116 for ; Thu, 16 May 2002 15:08:57 -0400 (EDT) Date: Thu, 16 May 2002 15:08:57 -0400 (EDT) From: "mer@chem.wayne.edu" To: CHEMISTRY@ccl.net Subject: Autodock mol2topdbqs error (fwd) Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Autodock users: I am getting the following error when i run the mol2topdbqs utility on a linux machine. I am using autodock 3.05. awk: cmd. line:77: fatal: expression for `<' redirection has null string value Someone had posted a similar problem on the ccl sometime ago but i could not find a response to that problem. Any help would be appreciated. Thanks. From chemistry-request@server.ccl.net Thu May 16 18:15:09 2002 Received: from hsc.usf.edu ([131.247.67.157]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4GMF9k08635 for ; Thu, 16 May 2002 18:15:09 -0400 Received: through eSafe SMTP Relay 1021397487; Thu May 16 18:11:25 2002 Received: from mindless.com (out.moffitt.usf.edu [131.247.182.200]) by hsc.usf.edu (8.9.3+Sun/8.9.3) with ESMTP id SAA04793 for ; Thu, 16 May 2002 18:15:00 -0400 (EDT) Message-ID: <3CE42F2C.1E077645@mindless.com> Date: Thu, 16 May 2002 18:14:04 -0400 From: David Smith X-Mailer: Mozilla 4.78 [en] (Win95; U) X-Accept-Language: en MIME-Version: 1.0 To: CCL Subject: Autodock: Ligand energy Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello Autodockers, I have a simple question for you this time regarding the energy of the ligand alone after docking. The results I get are: USER Final Docked Energy = -10.51 kcal/mol [=(1)+(2)] USER USER (1) Final Intermolecular Energy = -10.13 kcal/mol USER (2) Final Internal Energy of Ligand = -0.38 kcal/mol USER (3) Torsional Free Energy = +3.74 kcal/mol My Question is: Does the "Final Internal Energy of Ligand" represent the energy of the ligands particular conformation alone, apart from any outside energies such as from the macromolecule? In other words If I want to compare the energy of one docked ligand to the energy of another is this the calculations I could use to do that. thanks, Dave From chemistry-request@server.ccl.net Thu May 16 23:10:25 2002 Received: from biosino.org ([202.127.18.238]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4H3ANp19839 for ; Thu, 16 May 2002 23:10:24 -0400 Received: from mao [202.127.18.233] by biosino.org (SMTPD32-6.04) id A4834999011C; Fri, 17 May 2002 11:09:55 +0800 Date: Fri, 17 May 2002 11:12:4 +0800 From: "xmao@biosino.org" To: "chemistry@ccl.net" Subject: problem in frequency calculation X-mailer: FoxMail 3.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <200205171109869.SM00177@mao> Dear everyone: I met a problem when calculation the frequency using gamess-us, the following is the error, I hope you could help me to find out where the wrong is. Thanks in advance. Regards, mao ---------- ---------------------------------------------- TWO ELECTRON INTEGRAL DERIVATIVE CONTRIBUTIONS ---------------------------------------------- 253329 WORDS REQUIRED, 3000000 WORDS AVAILABLE ... WARNING ... THIS JOB MUST BE RESTARTED ... STEP CPU TIME = 96.46 TOTAL CPU TIME = 122.6 ( 2.0 MIN) TOTAL WALL CLOCK TIME= 124.0 SECONDS, CPU UTILIZATION IS 98.87% **** JOB HAS EXHAUSTED ITS CPU ALLOTMENT **** 120. 7 20 9 0 0 1 4 1 1 1 1 98 115000 EXECUTION OF GAMESS TERMINATED ABNORMALLY AT Fri May 17 10:02:34 2002 STEP CPU TIME = 0.00 TOTAL CPU TIME = 122.6 ( 2.0 MIN) TOTAL WALL CLOCK TIME= 124.0 SECONDS, CPU UTILIZATION IS 98.87% 2122700 WORDS OF DYNAMIC MEMORY USED *** ERROR TERMINATION *** IN COMPUTE PROCESS 0