From chemistry-request@server.ccl.net Tue Oct 29 05:54:14 2002 Received: from 263.sina.com ([202.106.182.141]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9TAsCD14181 for ; Tue, 29 Oct 2002 05:54:12 -0500 Received: (qmail 71648 invoked from network); 29 Oct 2002 10:44:38 -0000 Received: from unknown (HELO 263.sina.com) (162.105.161.3) by 202.106.182.141 with SMTP; 29 Oct 2002 10:44:38 -0000 Message-ID: <3DBE6B4A.8070205@263.sina.com> Date: Tue, 29 Oct 2002 19:04:42 +0800 From: Chen Hao User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.0.1) Gecko/20020830 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Jim Phillips , chemistry Subject: Re: CCL:Temperature Control in NAMD References: Content-Type: text/plain; charset=US-ASCII; format=flowed Content-Transfer-Encoding: 7bit Jim: My initial conformation derived from another equilibrate simulation by charmm in different temperature. I checked the potential energy and there's about 1300kcal/mol difference(from -20700kcal/mol to -22000kcal/mol). But after I minimized the initial conformation(500 steps CONJ, potential energy decrease to -32000kcal/mol), during the next equilibrate simulation, temperature decreased to about 150K very quickly(only 10 steps) and then increased to 298K very slowly. At last, the potential energy was about -22000kcal/mol. Do I have to heat the system firstly? If my system isn't stable in lower temperature, would the heat stage have any unreversed infulence in the structure? Chen Hao Jim Phillips wrote: >Hi, > >This sounds like your system wasn't minimized at the beginning of the >simulation, and you are seeing the initial conversion of potential to >kinetic energy. You should generally ignore the initial equilibration >period during analysis. > >-Jim > > >On Mon, 28 Oct 2002, Chen Hao wrote: > > > >>Dear all: >> I used temperature coupling to control temperature in NAMD. But when >>I set temperature for heat bath to 298K, I found after 2000-3000 steps >>the termerature could stabilize to 298K(I set inital temp. to 298K, >>during the simulation temp. increased to about 318K quickly and then >>decreased to 298K slowly). what's the matter? If I used it to do a >>equilibrate simulation(system is temperature sensitive), would the first >>few thousand steps have any influence? >> >>Chen Hao >> >> >> >> >> >> >> >> >> >> >> > > >-= 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 Tue Oct 29 00:59:27 2002 Received: from web12808.mail.yahoo.com ([216.136.174.43]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9T5xRD06586 for ; Tue, 29 Oct 2002 00:59:27 -0500 Message-ID: <20021029055927.55853.qmail@web12808.mail.yahoo.com> Received: from [210.14.43.25] by web12808.mail.yahoo.com via HTTP; Mon, 28 Oct 2002 21:59:27 PST Date: Mon, 28 Oct 2002 21:59:27 -0800 (PST) From: amor san juan Subject: AD3 in MPI To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi all, Have anyone successfully compiled Autodock3 in Message Passing Interface (MPI), a parallel computing environment? Kindly give me advice. Amor __________________________________________________ Do you Yahoo!? HotJobs - Search new jobs daily now http://hotjobs.yahoo.com/ From chemistry-request@server.ccl.net Mon Oct 28 18:17:30 2002 Received: from pscuxc.psc.edu ([128.182.66.177]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9SNHUD22439 for ; Mon, 28 Oct 2002 18:17:30 -0500 Received: from pscuxc.psc.edu (localhost.psc.edu [127.0.0.1]) by pscuxc.psc.edu (8.12.5/8.12.5) with ESMTP id g9SNHUT3031884 for ; Mon, 28 Oct 2002 18:17:31 -0500 (EST) Received: from localhost (wymore@localhost) by pscuxc.psc.edu (8.12.5/8.12.5/Submit) with ESMTP id g9SNHU9P028268 for ; Mon, 28 Oct 2002 18:17:30 -0500 (EST) Date: Mon, 28 Oct 2002 18:17:30 -0500 (EST) From: Troy Wymore To: Subject: CHARMM: Generating beta sheet structure Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello CHARMM people, I am having some difficulty doing something I thought would be trivial. I am trying to generate a peptide (~16 residues) to be in the beta sheet conformation with CHARMM. I have tried using CORMAN routines, modifying the topology file internal coordinates and such and can't get it quite right. Before struggling on too much, does anyone have a script to modify backbone dihedral angles or generate something close to what I need? Appreciate any help, Troy Wymore From chemistry-request@server.ccl.net Tue Oct 29 00:07:17 2002 Received: from smtp2.wiscmail.wisc.edu ([144.92.197.184]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9T57HD05364 for ; Tue, 29 Oct 2002 00:07:17 -0500 Received: from conversion-daemon.smtp2.doit.wisc.edu by smtp2.doit.wisc.edu (iPlanet Messaging Server 5.2 HotFix 0.8 (built Jul 12 2002)) id <0H4Q00H018R9WU@smtp2.doit.wisc.edu> for chemistry@ccl.net; Mon, 28 Oct 2002 23:05:58 -0600 (CST) Received: from chem71-49DHCP.chem.wisc.edu (chem71-49DHCP.chem.wisc.edu [128.104.71.49]) by smtp2.doit.wisc.edu (iPlanet Messaging Server 5.2 HotFix 0.8 (built Jul 12 2002)) with ESMTP id <0H4Q00GU88TXTZ@smtp2.doit.wisc.edu> for chemistry@ccl.net; Mon, 28 Oct 2002 23:05:57 -0600 (CST) Date: Mon, 28 Oct 2002 23:05:58 -0600 From: Qiang Cui Subject: Call for papers: 2003 Spring ACS symposium on Molecular motors To: chemistry@ccl.net Message-id: <1C77400C-EAFC-11D6-B08E-00039384826A@chem.wisc.edu> MIME-version: 1.0 X-Mailer: Apple Mail (2.482) Content-type: multipart/alternative; boundary="Boundary_(ID_e2wnH8MwEVF3o/hXJW5oZA)" --Boundary_(ID_e2wnH8MwEVF3o/hXJW5oZA) Content-type: text/plain; charset=ISO-8859-1; format=flowed Content-transfer-encoding: quoted-printable Call for papers (deadline, Nov. 1st). Understanding the physical chemistry of biomolecular motors A symposium to be held at the 2003 Spring ACS national meeting Physical chemistry Division, co-sponsored by the Computers in Chemistry=20= Division March, 23-27, 2003, New Orleans, Louisiana Organizers: Qiang Cui, Dept. of Chem. Univ. of Wisc., Madison, WI 53706=20 (cui@chem.wisc.edu) Carlos Bustamante, Dept. of Chem. Univ. of California, Berkeley, CA=20 (carlos@alice.berkeley.edu) Go to http://oasys.acs.org./oasys.htm Then follow the instructions. Make sure you select the Physical Chemistry Division, and our symposium. Summary: Molecular motors are fascinating nanomachines that interconvert energy=20= between chemical (e.g., ATP binding or hydrolysis) and mechanical forms.=20= The symposium brings together experts from three different research=20 disciplines including experimental biophysics (X-ray crystallography,=20 NMR, single molecule techniques, kinetics), microscopic simulations=20 (quantum and classical molecular dynamics) and theoretical=20 physics/chemistry (phenomenological modeling) to discuss the physical=20 and chemical principles that govern the functional mechanisms of=20 biomolecular motors. Questions of major interests include: how do=20 molecular motors move? What are significant chemical and conformational=20= intermediate states, what are their structures and in what sequence do=20= they occur? What are the rate-limiting steps? What are the driving=20 forces of molecular motors, and what are the enthalpic vs. entropic=20 contributions? What is the significance of stochastic characters of the=20= motor motions and how to define the efficiency of energy conversion? How=20= are the chemical events (nucleotide binding and hydrolysis) and=20 mechanical processes coupled? List of accepted speakers Biophysical (Structural, dynamical and catalytic aspects) W. S. Allison (UCSD), P. Boyer (UCLA), R. Cooke (UCSF), R. Fletterick (UCSF), R. H. Fillingame (UW, Madison), S. Gilbert (Pittsburghe), D.=20 Hackney (CMU), W. Junge (Osnabruck), R. Milligan (Scripps), I. Rayment (UW, Madison), = K. Kinosita (IMS), L. Sweeney (U. Penn), J. Weber (Rochester), M. Yoshida (Tokyo Inst.), J. E. Walker (MRC), W. Wriggers (Scripps) Microscopic simulations J. =C5qvist (Uppsala), C. L. Brooks (Scripps), J. Florian (USC), H. Grubmuller (Max Planck), M. Karplus (Harvard), J. Ma (Baylor), J. A. McCammon (UCSD), T. J. Minehardt (U. Colorado), T. Schlick (NYC), K. Schulten (UIUC), A. Warshel (USC) Phenomenological models M. Fisher (Maryland), H. Qian (Washington), J. Wang (Stony Brook) ________________________________________________________ Qiang Cui Assistant Professor of Chemistry =09 Department of Chemistry & Theoretical Chemistry Institute Rm. 8305-I University of Wisconsin, Madison 1101 University Ave Madison, WI 53706 Phone: 608-262-9801 Fax: 608-262-4782 =09 Email: cui@chem.wisc.edu Web: http://www.chem.wisc.edu/main/people/faculty/cui.html Group: http://kandinsky.chem.wisc.edu/~qiang ________________________________________________________ --Boundary_(ID_e2wnH8MwEVF3o/hXJW5oZA) Content-type: text/enriched; charset=ISO-8859-1 Content-transfer-encoding: quoted-printable Call for papers (deadline, Nov. 1st). Understanding the physical chemistry of biomolecular motors A symposium to be held at the 2003 Spring ACS national meeting=20 Physical chemistry Division, co-sponsored by the Computers in Chemistry Division March, 23-27, 2003, New Orleans, Louisiana Organizers: Qiang Cui, Dept. of Chem. Univ. of Wisc., Madison, WI 53706 (cui@chem.wisc.edu) Carlos Bustamante, Dept. of Chem. Univ. of California, Berkeley, CA (carlos@alice.berkeley.edu) Go to = 1A1A,1A1A,FFFFhttp://oasys.acs.org./oasys= .htm Then follow the instructions. Make sure you select the Physical Chemistry Division, and our symposium. Summary: TimesMolecular motors are fascinating nanomachines that interconvert energy between chemical (e.g., ATP binding or hydrolysis) and mechanical forms. The symposium brings together experts from three different research disciplines including experimental biophysics (X-ray crystallography, NMR, single molecule techniques, kinetics), microscopic simulations (quantum and classical molecular dynamics) and theoretical physics/chemistry (phenomenological modeling) to discuss the physical and chemical principles that govern the functional mechanisms of biomolecular motors. Questions of major interests include: how do molecular motors move? What are significant chemical and conformational intermediate states, what are their structures and in what sequence do they occur? What are the rate-limiting steps? What are the driving forces of molecular motors, and what are the enthalpic vs. entropic contributions? What is the significance of stochastic characters of the motor motions and how to define the efficiency of energy conversion? How are the chemical events (nucleotide binding and hydrolysis) and mechanical processes coupled? 0000,0000,DEDEList of accepted speakers Biophysical (Structural, dynamical and catalytic aspects) W. S. Allison (UCSD), P. Boyer (UCLA), R. Cooke (UCSF), R. Fletterick (UCSF), R. H. Fillingame (UW, Madison), S. Gilbert (Pittsburghe), D. Hackney (CMU),=20 W. Junge (Osnabruck), R. Milligan (Scripps), I. Rayment (UW, Madison), K. Kinosita (IMS), L. Sweeney (U. Penn), J. Weber (Rochester), M. Yoshida (Tokyo Inst.), J. E. Walker (MRC), W. Wriggers (Scripps) Microscopic simulations J. =C5qvist (Uppsala), C. L. Brooks (Scripps), J. Florian (USC), H. Grubmuller (Max Planck), M. Karplus (Harvard), J. Ma (Baylor), J. A. McCammon (UCSD), T. J. Minehardt (U. Colorado), T. Schlick (NYC), K. Schulten (UIUC), A. Warshel (USC) Phenomenological models M. Fisher (Maryland), H. Qian (Washington), J. Wang (Stony = Brook) = 4F4F,4343,FFFF________________________________= ________________________ Qiang Cui 4F4F,4343,FFFFAssistant Professor of Chemistry =09 Department of Chemistry & Theoretical Chemistry Institute Rm. 8305-I =20 University of Wisconsin, Madison 1101 University Ave Madison, WI 53706 =20 Phone: 608-262-9801 =20 Fax: 608-262-4782 =09 Email: cui@chem.wisc.edu Web: http://www.chem.wisc.edu/main/people/faculty/cui.html Group: http://kandinsky.chem.wisc.edu/~qiang ________________________________________________________ = --Boundary_(ID_e2wnH8MwEVF3o/hXJW5oZA)-- From chemistry-request@server.ccl.net Mon Oct 28 23:33:25 2002 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9T4XPD04897 for ; Mon, 28 Oct 2002 23:33:25 -0500 Received: from penguin.sunesis.com ([192.168.1.63]) by mercury.sunesis.com with Microsoft SMTPSVC(5.0.2195.2966); Mon, 28 Oct 2002 20:33:25 -0800 Date: Mon, 28 Oct 2002 20:33:25 -0800 (PST) From: "Warren L. DeLano" To: Luca Fenu cc: , Subject: Re: CCL:scripting pymol In-Reply-To: <3DBD8A72.791B153C@soton.ac.uk> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-OriginalArrivalTime: 29 Oct 2002 04:33:25.0389 (UTC) FILETIME=[521AF3D0:01C27F04] Luca, For future reference, please direct technical PyMOL questions like this to the PyMOL mailing list. (See MailLists on http://www.pymol.org) Over the past couple of years, we've built up an active community of nearly 300 PyMOL users who are there to learn and to help each other get the most out of this free/open-source molecular viewer. Please join in! The answer to your question is: Launch PyMOL with a "-p" command-line argument. PyMOL will then listen for commands on standard input. Using a Perl pipe, you can then control PyMOL interactively and send commands as required in order to load new structures, change the view, color, and so on. The only trick with Perl is that you need to turn autoflush on so that commands get passed along right away. use FileHandle; open(FILE,"|pymol -p"); FILE->autoflush(1); print FILE "load \$PYMOL_PATH/test/dat/pept.pdb\n"; while(1) { sleep 0.2; print FILE "turn x,5\n"; } Please excuse my non-OOP-0Perl4-vintage example...I've been a Python addict for some time now. If you want PyMOL to be just a minimal molecular display window, then consider launching PyMOL as: pymol -qpxif 0 This will make PyMOL open a single window with no visible GUI, text, or controls. Cheers, Warren On Mon, 28 Oct 2002, Luca Fenu wrote: > Dear all, > > I need to scan and make a choice about a list of molecules. does anyone > knows how to send command to pymol through a perl or shell script? I've > read pymol's manual, and it's possible to pass pymol some scripts, from > its internal shell. but I don't know how to pass commands to it from > another program. starting the process in foreground and feeding the > command from the stdout of perl to the stdin of pymol doesn't work. I > think pymol use another filehandle for aquiring commands. how can I > avoid to restar a new pymol for every molecule? > any suggestion? many thanks > > luca > > > From chemistry-request@server.ccl.net Mon Oct 28 21:37:18 2002 Received: from smtp02.sohu.com ([61.135.132.105]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9T2bFD02182 for ; Mon, 28 Oct 2002 21:37:17 -0500 Received: from PC12 (unknown [202.127.19.236]) by smtp02.sohu.com (Postfix) with ESMTP id CE1EA6A902 for ; Tue, 29 Oct 2002 10:35:15 +0800 (CST) Date: Tue, 29 Oct 2002 10:38:58 +0800 From: "=?GB2312?Q?=C1=F5=D6=CE=B9=FA?=" To: "CHEMISTRY@ccl.net" Subject: Question about Dock4.0 X-mailer: Foxmail 4.1 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon730105378667_=====" Message-Id: <20021029023515.CE1EA6A902@smtp02.sohu.com> This is a multi-part message in MIME format. --=====000_Dragon730105378667_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: quoted-printable Dear CCLers, =09I'm using Dock4.0 to dock a small molecule into a receptor.I= have the crystal structure of the complex of them.So I extracted= the small molecule from complex and docked.However,the result= was not satisfying.The RMSD was always over 6.0A.I don't know= which key parameter I should change first.Could anybody tell me= please?Thanks! =09=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=A12002-10-29 --=====000_Dragon730105378667_===== 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 s6AoDBSjczW9atrcibicmQPZ229yS0AGNUEGCkIKghYiBgGQkZIKi4wHBoWSmgEGjHOXBZucnUov 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from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus2.its.rochester.edu (8.11.6/8.11.6) with SMTP id g9TFmBH21779 for ; Tue, 29 Oct 2002 10:48:11 -0500 (EST) Received: from frenkel.chem.rochester.edu (frenkel.chem.rochester.edu [128.151.195.84]) by mail.rochester.edu (8.12.4/8.12.1) with ESMTP id g9TFmAjj004446 for ; Tue, 29 Oct 2002 10:48:10 -0500 (EST) Content-Type: text/plain; charset="us-ascii" From: wei Reply-To: weiz@mail.rochester.edu Organization: university of rochester To: chemistry@ccl.net Subject: ligantion parameters in charmm Date: Tue, 29 Oct 2002 10:46:28 +0000 User-Agent: KMail/1.4.1 MIME-Version: 1.0 Message-Id: <200210291046.28410.weiz@mail.rochester.edu> Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g9TFmCD21341 Hi, all: I want to use CHARMM to simulate a protein-pigment aggregate, in this aggregate the MG 2+ of the pigment is liganded to a His residue of the protein, How can I represent this in my .rtf and .prm file? I couldn't find any parameters about MG-N binding in charmm. Thanks for the help. wei zhuang From chemistry-request@server.ccl.net Tue Oct 29 11:15:20 2002 Received: from ns1.scripps.edu ([192.42.82.59]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TGFKr22172 for ; Tue, 29 Oct 2002 11:15:20 -0500 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns1.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g9TGFJs06929 for ; Tue, 29 Oct 2002 08:15:19 -0800 (PST) Received: from relay1.scripps.edu(137.131.200.29) by antigen.scripps.edu via csmap id 8155; Tue, 29 Oct 2002 08:13:27 -0800 (PST) Received: from renoir.scripps.edu (renoir.scripps.edu [137.131.252.25]) by relay1.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g9TGFDA19536; Tue, 29 Oct 2002 08:15:13 -0800 (PST) Received: (from crowley@localhost) by renoir.scripps.edu (8.9.2/TSRI-3.0.1) id IAA105987; Tue, 29 Oct 2002 08:15:13 -0800 (PST) Date: Tue, 29 Oct 2002 08:15:13 -0800 (PST) From: Michael Crowley Message-Id: <200210291615.IAA105987@renoir.scripps.edu> To: , Troy Wymore Subject: Re: CCL:CHARMM: Generating beta sheet structure Troy, Look in the test suite, there is a beta sheet image test: test/c20test/imbetash.inp That might help. Mike From chemistry-request@server.ccl.net Tue Oct 29 11:28:57 2002 Received: from cornell.edu ([132.236.56.6]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TGSvr22459 for ; Tue, 29 Oct 2002 11:28:57 -0500 Received: from cornell.edu (lock.lassp.cornell.edu [128.84.241.198]) by cornell.edu (8.9.3/8.9.3) with ESMTP id LAA07851 for ; Tue, 29 Oct 2002 11:28:58 -0500 (EST) Sender: cc236@cornell.edu Message-ID: <3DBEB749.341BCC52@cornell.edu> Date: Tue, 29 Oct 2002 11:28:57 -0500 From: Connie Chang X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.2.19-6.2.16smp i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Getting electronic spectrum info from Gaussian Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi -- I was wondering what is the best way to get electronic spectrum information from Gaussian98? I've read in the manual that you can use the CI singles method. Are there other ways to do it? And do I need to do something with my structure first before using the CI singles method such as geometrically minimizing it with HF? I've already minimized my structure with PM3. Finally, if I really have no idea what the spectrum might look like, and I am interested in the first 5 levels or so, is there a fool-proof way to get these? Does it just require specifying a higher number for the Nstates option? Thanks, Connie From chemistry-request@server.ccl.net Tue Oct 29 12:30:50 2002 Received: from bfp.cc.purdue.edu ([128.210.189.30]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9THUnr23985 for ; Tue, 29 Oct 2002 12:30:49 -0500 Received: from bfp.cc.purdue.edu (localhost [127.0.0.1]) by bfp.cc.purdue.edu (8.12.5/8.12.5) with ESMTP id g9THUnf0001043 for ; Tue, 29 Oct 2002 12:30:49 -0500 (EST) Received: from localhost (bfp@localhost) by bfp.cc.purdue.edu (8.12.5/8.12.5/Submit) with ESMTP id g9THUnGi001040 for ; Tue, 29 Oct 2002 12:30:49 -0500 (EST) X-Authentication-Warning: bfp.cc.purdue.edu: bfp owned process doing -bs Date: Tue, 29 Oct 2002 12:30:49 -0500 (EST) From: Bryan Putnam X-X-Sender: bfp@bfp.cc.purdue.edu To: CCL Subject: Building g98A11.3 with 64-bit integers Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Has anyone had success in building g98A11.3 with large-file support, using 64-bit integers, on a Red Hat Linux (7.3) Pentium machine? I understand that only the 32-bit version of g98 is supported by Gaussian, Inc. on the Pentium, which has a 32-bit architecture. I have been successful in using large files (>2GB) in a small Fortran program, compiled with pgf77 (ver. 4.0), and specifying "-L/usr/pgi/linux86/liblf" on the link. Therefore, I suppose getting g98 to handle files larger than 2GB on our system (actually larger than 16GB since you can break up the RWF file into 8 pieces of 2GB) is simply a matter of "tweaking" the g98 code and adjusting build options. However, I'm beginning to think it might be a bit more complicated then simply playing around with options such as I8CPP = -DI64 I8FLAG = -i8 -r8 LIBS = -L/usr/pgi/linux86/liblf since the resulting g98 Links immediately fail when run, although the build does complete without errors. Thanks for any advice or experience with this, Bryan -- Bryan Putnam, IT Research Computing Services Mathematical Sciences Building Email: bfp@purdue.edu 150 North University Street Phone: 765.496.8225 West Lafayette, IN 47907-2068 Fax: 765.494.0566 http://www.purdue.edu/ITaP http://www-rcd.cc.purdue.edu/~bfp/ From chemistry-request@server.ccl.net Tue Oct 29 14:11:43 2002 Received: from ks.uiuc.edu ([130.126.120.73]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TJBhr25565 for ; Tue, 29 Oct 2002 14:11:43 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by ks.uiuc.edu (8.11.2/8.11.2) with ESMTP id g9TJBhB09500; Tue, 29 Oct 2002 13:11:43 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.10.2+Sun/8.9.1) with ESMTP id g9TJBJZ16864; Tue, 29 Oct 2002 13:11:20 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Tue, 29 Oct 2002 13:11:19 -0600 (CST) From: Jim Phillips To: Chen Hao cc: chemistry Subject: Re: CCL:Temperature Control in NAMD In-Reply-To: <3DBE6B4A.8070205@263.sina.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi again, Please look at the PSF and PDB input files you're giving NAMD in VMD, to see it something looks strange. I'm guessing the atom order between the two files is different for a couple of atoms (NAMD and VMD expect it to be the same, but don't check), resulting in the high initial energy. -Jim On Tue, 29 Oct 2002, Chen Hao wrote: > Jim: > My initial conformation derived from another equilibrate simulation by > charmm in > different temperature. I checked the potential energy and there's about > 1300kcal/mol > difference(from -20700kcal/mol to -22000kcal/mol). But after I minimized > the initial > conformation(500 steps CONJ, potential energy decrease to > -32000kcal/mol), during the > next equilibrate simulation, temperature decreased to about 150K very > quickly(only 10 > steps) and then increased to 298K very slowly. At last, the potential > energy was about > -22000kcal/mol. > Do I have to heat the system firstly? If my system isn't stable in lower > temperature, > would the heat stage have any unreversed infulence in the structure? > > Chen Hao > Jim Phillips wrote: > > >Hi, > > > >This sounds like your system wasn't minimized at the beginning of the > >simulation, and you are seeing the initial conversion of potential to > >kinetic energy. You should generally ignore the initial equilibration > >period during analysis. > > > >-Jim > > > > > >On Mon, 28 Oct 2002, Chen Hao wrote: > > > > > > > >>Dear all: > >> I used temperature coupling to control temperature in NAMD. But when > >>I set temperature for heat bath to 298K, I found after 2000-3000 steps > >>the termerature could stabilize to 298K(I set inital temp. to 298K, > >>during the simulation temp. increased to about 318K quickly and then > >>decreased to 298K slowly). what's the matter? If I used it to do a > >>equilibrate simulation(system is temperature sensitive), would the first > >>few thousand steps have any influence? > >> > >>Chen Hao > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > >> > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > -= 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 Tue Oct 29 11:54:31 2002 Received: from cpimssmtpu03.email.msn.com ([207.46.181.79]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TGsVr23042 for ; Tue, 29 Oct 2002 11:54:31 -0500 Received: from catchcafmsn ([68.129.23.244]) by cpimssmtpu03.email.msn.com with Microsoft SMTPSVC(5.0.2195.4617); Tue, 29 Oct 2002 08:53:08 -0800 Message-ID: <000901c27f6c$1ccd3040$f4178144@com> Reply-To: "Mauricio Cafiero" From: "Mauricio Cafiero" To: , "guest" Subject: uncertainty principle Date: Tue, 29 Oct 2002 09:56:19 -0700 X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-OriginalArrivalTime: 29 Oct 2002 16:53:08.0984 (UTC) FILETIME=[A8CA1780:01C27F6B] hello: While the UP is often described in terms of an experiment, it is in fact independant of experiment. This uncertainty is inherent in the system itself and will manifest itself no matter how accurate your microscope is. This whole experiment business is put in to help people visualize it. Read a book on localization of wave packets and this should help. Mauricio Cafiero Doctoral Candidate: Theoretical and Computational Quantum Chemistry University Of Arizona From chemistry-request@server.ccl.net Tue Oct 29 12:05:57 2002 Received: from laplinux.dcfe.unimi.it ([159.149.31.26]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TH5vr23224 for ; Tue, 29 Oct 2002 12:05:57 -0500 Received: from laplinux.dcfe.unimi.it (localhost [127.0.0.1]) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/SuSE Linux 0.6) with ESMTP id g9TH5YuR032593 for ; Tue, 29 Oct 2002 18:05:34 +0100 Received: from localhost (acontini@localhost) by laplinux.dcfe.unimi.it (8.12.3/8.12.3/Submit) with ESMTP id g9TH5Yfs032590 for ; Tue, 29 Oct 2002 18:05:34 +0100 X-Authentication-Warning: laplinux.dcfe.unimi.it: acontini owned process doing -bs Date: Tue, 29 Oct 2002 18:05:34 +0100 (CET) From: Alessandro Contini X-X-Sender: acontini@laplinux.dcfe.unimi.it To: CCL Subject: CPMD 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 g9TH5vr23225 Hi, I'd like to start using the ab-initio molecular dynamics package CPMD. I tried to read the manual but I found it pretty criptic. Does anybody knows if there are some good tutorials available or is anybody so kind to send me an example of input file for an explicit solvent md of a small molecule? Thanks a lot Alessandro Dott. Alessandro Contini Istituto di Chimica Organica "Alessandro Marchesini" Facoltà di Farmacia Università degli Studi di Milano Via Venezian, 21 20133 Milano Tel. +390250314480 Fax +390250314476 http://users.unimi.it/istchimorg/pagconthtm.htm From chemistry-request@server.ccl.net Tue Oct 29 13:12:26 2002 Received: from web13407.mail.yahoo.com ([216.136.175.65]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g9TICQr24714 for ; Tue, 29 Oct 2002 13:12:26 -0500 Message-ID: <20021029181225.82763.qmail@web13407.mail.yahoo.com> Received: from [67.17.165.2] by web13407.mail.yahoo.com via HTTP; Tue, 29 Oct 2002 10:12:25 PST Date: Tue, 29 Oct 2002 10:12:25 -0800 (PST) From: quch quch Subject: Re: CCL:Question about Dock4.0 To: zgliu@sohu.com Cc: chemistry@ccl.net In-Reply-To: <20021029023515.CE1EA6A902@smtp02.sohu.com> MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii you may try other docking programs. --- 隸笥弊 wrote: > Dear CCLers, > I'm using Dock4.0 to dock a small molecule into a > receptor.I have the crystal structure of the complex > of them.So I extracted the small molecule from > complex and docked.However,the result was not > satisfying.The RMSD was always over 6.0A.I don't > know which key parameter I should change first.Could > anybody tell me please?Thanks! > ﹛﹛﹛﹛﹛﹛﹛﹛zgliu@sohu.com > ﹛﹛﹛﹛﹛﹛﹛﹛﹛﹛2002-10-29 > > ATTACHMENT part 2 image/gif name=fox.gif __________________________________________________ Do you Yahoo!? HotJobs - Search new jobs daily now http://hotjobs.yahoo.com/ From chemistry-request@server.ccl.net Tue Oct 29 11:53:12 2002 Received: from TheWorld.com ([199.172.62.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TGrCr23017 for ; Tue, 29 Oct 2002 11:53:12 -0500 Received: from world.std.com (payne@world-f.std.com [199.172.62.5]) by TheWorld.com (8.9.3/8.9.3) with ESMTP id LAA27436 for ; Tue, 29 Oct 2002 11:53:11 -0500 Received: (from jle@localhost) by world.std.com (8.9.3/8.9.3) id LAA28210 for chemistry@ccl.net; Tue, 29 Oct 2002 11:53:07 -0500 (EST) Date: Tue, 29 Oct 2002 11:53:07 -0500 (EST) From: Joe M Leonard Message-Id: <200210291653.LAA28210@world.std.com> To: chemistry@ccl.net Subject: MolVol/Dodd & Theodorou Does anybody have this program to calculate area/volume, or a pointer to where one might get this program? I've seen older stuff in the CCL archives, but nothing that recent... Thanks in advance! Joe Leonard P.S. Alternatives welcome, too! P.P.S. Mac-related question will be summarized RSN, but the bottom line seems to be "don't buy it for the horsepower"... (jle@theworld.com) From chemistry-request@server.ccl.net Tue Oct 29 15:22:02 2002 Received: from smtp.targetedmolecules.com ([66.52.63.229]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TKM1r27116 for ; Tue, 29 Oct 2002 15:22:01 -0500 Received: from bioinfo01 ([192.168.1.54]) by smtp.targetedmolecules.com (8.11.0/8.11.0) with SMTP id g9TKLsj14853 for ; Tue, 29 Oct 2002 12:21:54 -0800 Reply-To: From: "Ruben E. Venegas" To: Subject: Stereo for PC Date: Tue, 29 Oct 2002 12:21:55 -0800 Message-ID: <001001c27f88$d41c27d0$3601a8c0@TARGETEDMOLECULES.COM> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook CWS, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal Hi: What people are using for viewing structures in 3-D stereo on a PC (W2K machine) ? I am interested in software and hardware solutions. I want to manipulate structures in stereo mode. For example, I'd like to manually overlay two or more molecules. Thank you for your responses Ruben Venegas From chemistry-request@server.ccl.net Tue Oct 29 14:56:59 2002 Received: from atom.ecn.purdue.edu ([128.46.108.94]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TJuxr26701 for ; Tue, 29 Oct 2002 14:56:59 -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 g9TJuv07002458 for ; Tue, 29 Oct 2002 14:56:57 -0500 (EST) Message-ID: <3DBEE809.F4D7E0C5@ecn.purdue.edu> Date: Tue, 29 Oct 2002 14:56:57 -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: CCL Subject: damped molecular dynamics References: Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Virus-Scanned-ECN: by AMaVIS version 11 (http://amavis.org/) Hello CCL'ers, I need some help damped molecular dynamics that I use in two programs. The programs allow for specification of a friction coefficient and time step. My questions are: 1) What is a good strategy to reach the relaxed structure? My runs either do one of two things. They either will eventually 'die' to zero kinetic energy with little change in atom positions, or will slow down, then oscillate and explode as the kinetic energy takes off. Ideally the kinetic energy should die down as the relaxed structure is reached, right? This isn't always the case. 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 Tue Oct 29 15:13:37 2002 Received: from prserv.net ([32.97.166.34]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TKDbr27046 for ; Tue, 29 Oct 2002 15:13:37 -0500 Received: from attglobal.net (slip-12-64-14-181.mis.prserv.net[12.64.14.181]) by prserv.net (out4) with SMTP id <2002102920133620403noo7ge>; Tue, 29 Oct 2002 20:13:36 +0000 Message-ID: <3DBEA5F4.68D42855@attglobal.net> Date: Tue, 29 Oct 2002 15:15:00 +0000 From: jmmckel@attglobal.net Reply-To: jmmckel@attglobal.net X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: Connie Chang CC: chemistry@ccl.net Subject: Re: CCL:Getting electronic spectrum info from Gaussian References: <3DBEB749.341BCC52@cornell.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I've spent literally decades on related problems :-) For organic systems the most reliable way in Gaussian is to optimize the geometry with something like B3LYP/6-31G*, and then do ZINDO with all single excitations. Use of semi empirical geometries should be used with the utmost caution, particularly if molecules are non-planar... they are "cheap," but.... Grins, John McKelvey Connie Chang wrote: > Hi -- > > I was wondering what is the best way to get electronic spectrum > information from Gaussian98? > > I've read in the manual that you can use the CI singles method. Are > there other ways to do it? And do I need to do something with my > structure first before using the CI singles method such as geometrically > minimizing it with HF? I've already minimized my structure with PM3. > > Finally, if I really have no idea what the spectrum might look like, and > I am interested in the first 5 levels or so, is there a fool-proof way > to get these? Does it just require specifying a higher number for the > Nstates option? > > Thanks, > Connie > > -= 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 Tue Oct 29 16:19:48 2002 Received: from copland.udel.edu ([128.175.13.92]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9TLJmr28381 for ; Tue, 29 Oct 2002 16:19:48 -0500 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.12.6/8.12.6) with ESMTP id g9TLJm6F019401 for ; Tue, 29 Oct 2002 16:19:48 -0500 (EST) Message-Id: <200210292119.g9TLJm6F019401@copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Tue, 29 Oct 2002 16:18:49 -0500 Subject: GAMESS US:basis sets and MOREAD From: "Olga Dmitrenko" To: CHEMISTRY@ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit Dear CClers, It's a question for GAMESS/GAUSSIAN users. I am trying to re-optimize the transition structure with larger basis set (with GAMESS). Similarly to what I did before when using g98, I was trying to read molecular orbitals from previous calculation done with smaller basis set. I can not do it in Gamess. I am putting the orbitals from RHF/6-31G* into $VEC group. But I am getting an error msg: FORMING THE "STANDARD FOCK OPERATOR" IN DIRECT AO INTEGRAL MODE... *** ERROR *** ATTEMPT TO READ A DAF RECORD THAT WAS NEVER WRITTEN. RECORD NUMBER 16 OF LENGTH 1711 DOES NOT EXIST. CHECK -PROG.DOC- FOR A LIST OF DIRECT ACCESS FILE CONTENTS Here is ethylene input which I use for the test: $CONTRL SCFTYP=MCSCF RUNTYP=OPTIMIZE $END $SYSTEM TIMLIM=6000000 $END $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 NPFUNC=1 DIFFSP=.TRUE. $END $GUESS GUESS=MOREAD NORB=38 $END $DET NCORE=6 NACT=4 NELS=4 $END $STATPT HESS=READ $END $FORCE PURIFY=.TRUE. $END $MCSCF FULLNR=.true. $END $DATA Title goes here C1 C 6.0 -0.00118 -0.67739 0.00029 C 6.0 0.00244 0.67920 0.00281 H 1.0 -0.34038 -1.24992 -0.87390 H 1.0 -0.33487 1.25172 -0.87225 H 1.0 0.33443 -1.25655 0.87156 H 1.0 0.33326 1.24386 0.85599 $END --- OPTIMIZED RHF MO-S --- GENERATED AT Tue Oct 29 16:04:35 2002 E= -78.0317181226, E(NUC)= 33.6898229925 $VEC 1 1 7.05969046E-01 1.93391836E-02 1.33102588E-07-1.46317608E-04 1.32501938E-06 1 2-5.37415328E-03-8.57895899E-07 7.40478715E-04-6.71078979E-06-1.86940455E-03 1 3-1.31112269E-03-1.69132356E-03-2.08747231E-08 9.34926162E-05-3.50681631E-06 1 4 7.01483067E-01 1.92131948E-02-2.09775887E-07 1.47626169E-04-1.20184339E-06 1 5-5.30162275E-03 1.06525481E-06-7.52418391E-04 6.16205533E-06-1.85851957E-03 1 6-1.30465879E-03-1.68288232E-03-8.29155038E-08 9.21976862E-05-3.56623682E-06 1 7-1.41301011E-04 1.49040104E-03-1.40853161E-04 1.48095367E-03-1.41074470E-04 1 8 1.49071003E-03-1.40760238E-04 1.48089957E-03 2 1-7.01988278E-01-1.97408672E-02 2.44435177E-07-1.83476256E-04 1.36070238E-06 2 2 1.11733459E-02-2.43361904E-06 1.67381185E-03-1.33317017E-05 1.72224119E-03 2 3 9.81832178E-04 1.33987177E-03-6.68659234E-07-2.00744834E-04 3.12876471E-06 2 4 7.06470970E-01 1.98637729E-02 2.97522856E-07-1.82237831E-04 1.56911008E-06 2 5-1.12078929E-02-2.01050700E-06 1.66830556E-03-1.42338849E-05-1.73422402E-03 2 6-9.90071516E-04-1.35073720E-03 4.25914203E-07 2.01326009E-04-3.29814644E-06 2 7 6.48371363E-05-1.53732716E-03-6.56774411E-05 1.54727923E-03 6.46977266E-05 2 8-1.53786356E-03-6.56203061E-05 1.54741608E-03 and so on I would be much grateful if somebody will tell me that it is not possible in gamess or it is possible (but how?). Olga Dmitrenko From chemistry-request@server.ccl.net Tue Oct 29 19:40:46 2002 Received: from bh.knu.ac.kr ([155.230.10.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g9U0ekn00795 for ; Tue, 29 Oct 2002 19:40:46 -0500 Received: from bh.kyungpook.ac.kr (bh [155.230.10.2]) by bh.knu.ac.kr (8.11.2/8.11.2) with SMTP id g9U0WtE02770 for ; Wed, 30 Oct 2002 09:32:55 +0900 (KST) Received: from cchoi (p181_53.kyungpook.ac.kr [155.230.181.53]) by bh.kyungpook.ac.kr with SMTP (MailShield v2.04 - SOLARIS/SPARC Jul 18 2001 17:16:48); Wed, 30 Oct 2002 09:32:55 +0900 From: "Cheol Ho Choi" To: Subject: g98 + pgf77 4.0-2 compile problem Date: Wed, 30 Oct 2002 09:40:32 +0900 Message-ID: <000d01c27fac$f4797c20$35b5e69b@cchoi> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.4024 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1106 Importance: Normal Dear CCLers, I'm having a problem in compiling g98-A11 with pgf77 version 4.0-2. I got pgf77 -O0 -tp p6 -c eroute.f PGFTN-S-0067-Too many data constants in initialization statement (eroute.f: 815) PGFTN-S-0067-Too many data constants in initialization statement (eroute.f: 829) 0 inform, 0 warnings, 2 severes, 0 fatal for eroute PGFTN/x86 Linux/x86 4.0-2: compilation completed with severe errors make[2]: *** [eroute.o] Error 2 make[2]: Leaving directory `/home/share/src/g98/g98/temp-l1' It looks to me that pgf77 cannot handle too many constants. Does anybody know how to fix it? Thanks in advance. Cheol Cheol Ho Choi, Assistant Professor Dept. of Chemistry Kyungpook National University 702-701 Daegu, South Korea email: cchoi@knu.ac.kr web: knu.ac.kr/~cchoi TEL: 82-53-950-5332 FAX: 82-53-950-6330