From chemistry-request@server.ccl.net Thu May 23 02:23:44 2002 Received: from igc.phys.chem.ethz.ch ([129.132.218.130]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4N6Nh013379 for ; Thu, 23 May 2002 02:23:44 -0400 Received: from igc.phys.chem.ethz.ch (humagne [129.132.218.162]) by igc.phys.chem.ethz.ch (8.11.4/8.11.4) with ESMTP id g4N6Nbx07344; Thu, 23 May 2002 08:23:37 +0200 (MEST) Sender: portmann@igc.phys.chem.ethz.ch Message-ID: <3CEC8AE9.E4281EBE@igc.phys.chem.ethz.ch> Date: Thu, 23 May 2002 08:23:37 +0200 From: Stefan Portmann X-Mailer: Mozilla 4.76 [en] (X11; U; SunOS 5.8 sun4u) X-Accept-Language: en MIME-Version: 1.0 To: temper CC: chemistry@ccl.net Subject: Re: CCL:NBO_PLOTS References: <001201c20194$10236d60$5e40cf9b@chem.auth.gr> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi MOLEKEL is able to visualize NBOs calculated with Gaussian. Please check http://www.cscs.ch/molekel/ Stefan -- Dr. Stefan Portmann Physical Chemistry ETH Hoenggerberg, HCI G229 CH-8093 Zurich Switzerland Phone: +41 (0) 1 632 57 82 Fax: +41 (0) 1 632 16 15 e-mail: portmann@igc.phys.chem.ethz.ch WWW: http://igc.ethz.ch/portmann/ From chemistry-request@server.ccl.net Thu May 23 03:21:43 2002 Received: from secure.webhotel.net ([217.116.225.80]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4N7Lg016910 for ; Thu, 23 May 2002 03:21:42 -0400 Received: (qmail 16312954 invoked from network); 23 May 2002 07:22:39 -0000 Received: from unknown (HELO localhost.localdomain) (217.116.225.1) by mail.webhotel.net with SMTP; 23 May 2002 07:22:39 -0000 Subject: Re: CCL:diffusion coefficient from mean square displacement From: Kenneth Geisshirt To: chemistry@ccl.net In-Reply-To: <1022094365.3cebec1dbcf39@web-mail2.uibk.ac.at> References: <1022094365.3cebec1dbcf39@web-mail2.uibk.ac.at> Content-Type: text/plain; charset=ISO-8859-1 X-Mailer: Ximian Evolution 1.0.3 Date: 23 May 2002 09:21:59 +0200 Message-Id: <1022138519.11998.10.camel@Douglas> Mime-Version: 1.0 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g4N7Lh016911 On Wed, 2002-05-22 at 21:06, Hannes Loeffler wrote: > But what does "long time" mean? I observe that the MSD curve becomes nearly > linear after a few pico second but after some pico seconds later the line starts > to rise again with an obviously larger slope. Does this tell me anything about > the quality of the potential used? Should I be concerned about the "non-linear" > MSD curve? You don't explain how you compute the displacement and in what geometry and boundary conditions you're working. With periodic boundary conditions you have to take that into account i.e., when a particle moves out of the simulation box (and comes back on the other side), remember that the displacement must be added the box length. Estimating the slope will give you the covariance matrix (see e.g. GNU Scientific Library . Using that matrix you have a measure of the error bar and is the error bar too large, you were impatient ;-). Kneth -- Kenneth Geisshirt, M.Sc., Ph.D. http://kenneth.geisshirt.dk Grøndals Parkvej 2A, 3. sal kenneth@geisshirt.dk DK-2720 Vanløse +45 38 87 78 38 From chemistry-request@server.ccl.net Thu May 23 08:58:49 2002 Received: from prserv.net ([32.97.166.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NCwn001126 for ; Thu, 23 May 2002 08:58:49 -0400 Received: from attglobal.net (slip-32-101-104-47.in.us.prserv.net[32.101.104.47]) by prserv.net (out1) with SMTP id <20020523125848201067eq2pe>; Thu, 23 May 2002 12:58:48 +0000 Message-ID: <3CECA16E.70A4C41C@attglobal.net> Date: Thu, 23 May 2002 07:59:42 +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: Chemistry@ccl.net Subject: Direct CI Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello, I am looking into doing an All-Singles, or perhaps smaller, CI [CIS] using a direct CI method. I am purely guessing that this would avoid storage of the 2-e integrals over MO's. Pointers to a code available, and/or references would be most appreciated. Will post results. Regards, John McKelvey From chemistry-request@server.ccl.net Thu May 23 08:14:20 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NCEK030834 for ; Thu, 23 May 2002 08:14:20 -0400 Received: from cornell.edu ([128.84.182.122]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id IAA07000; Thu, 23 May 2002 08:14:16 -0400 (EDT) Sender: richard@cornell.edu Message-ID: <3CECDD17.8058173D@cornell.edu> Date: Thu, 23 May 2002 08:14:15 -0400 From: Richard Gillilan X-Mailer: Mozilla 4.77 [en] (X11; U; Linux 2.4.16 i686) X-Accept-Language: en MIME-Version: 1.0 To: Hannes Loeffler CC: chemistry@ccl.net Subject: Re: CCL:diffusion coefficient from mean square displacement References: <1022094365.3cebec1dbcf39@web-mail2.uibk.ac.at> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hannes Loeffler wrote: I assume you are using periodic boundary conditions for the bulk liquid. Make sure you are treating periodic boundary conditions correctly in the calculation of the MSD. Richard Gillilan MacCHESS Cornell > > Hello, > > I'm currently trying to obtain the diffusion coefficient from the mean square > displacement (as a test case I simulated pure water). The diffusion coefficient > may than be derived from the long time behavior of the MSD curve (slope). > > But what does "long time" mean? I observe that the MSD curve becomes nearly > linear after a few pico second but after some pico seconds later the line starts > to rise again with an obviously larger slope. Does this tell me anything about > the quality of the potential used? Should I be concerned about the "non-linear" > MSD curve? > > Hannes. > > -- > Hannes Loeffler | tel: +43-(0)512-507-5166 | fax: +43-(0)512-507-2714 > http://www-c724.uibk.ac.at/staff/loeffler/ | mailto:Hannes.Loeffler@uibk.ac.at > Institute for General, Inorganic and Theoretical Chemistry > University of Innsbruck, Austria > > -= 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 23 04:12:07 2002 Received: from hotmail.com ([207.68.163.178]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4N8C7019900 for ; Thu, 23 May 2002 04:12:07 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 23 May 2002 01:12:02 -0700 Received: from 193.146.42.31 by sea1fd.sea1.hotmail.msn.com with HTTP; Thu, 23 May 2002 08:12:01 GMT X-Originating-IP: [193.146.42.31] From: "Mus Musculus" To: CHEMISTRY@ccl.net Subject: Another error message in Gaussian98 Date: Thu, 23 May 2002 10:12:01 +0200 Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1; format=flowed Message-ID: X-OriginalArrivalTime: 23 May 2002 08:12:02.0063 (UTC) FILETIME=[849251F0:01C20231] Dear CCL'rs, I'm sorry to annoy you with this kind of mails, but lately I have been obtaining error messages like this one: " JPrint(4)<0 in NAOANL. Error termination via Lnk1e in C:\G98W\l607.exe. " when trying to make the NBO analysis of a transition state. Can anyone tell me what does this error mean? Thank you Viv _________________________________________________________________ Hable con sus amigos en línea, pruebe MSN Messenger: http://messenger.msn.es From chemistry-request@server.ccl.net Thu May 23 10:15:05 2002 Received: from ovlev1.mdche.u-szeged.hu ([160.114.101.231]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4NEF4004899 for ; Thu, 23 May 2002 10:15:04 -0400 Received: from localhost by ovlev1.mdche.u-szeged.hu (5.65v3.2/1.1.10.5/19Nov99-0914AM) id AA16957; Thu, 23 May 2002 16:20:48 +0100 Date: Thu, 23 May 2002 16:20:48 +0100 (GMT+0100) From: Csaba Hetenyi To: chemistry@ccl.net Subject: atomic dft CODE Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Could you please recommend a free non-relativistic atomic FREE program CODE for DFT. (I have the Hellmann-Skillman code.) Thanks in advance. Best wishes, Csaba _______________________________________ Csaba Hetenyi, M.Sc., Ph.D. student University of Szeged Dept. of Medical Chemistry Addr.:H-6720 Szeged, Dom ter 8, Hungary Tel.: +36-62545147 or: +36-62545136 Fax.: +36-62545971 From chemistry-request@server.ccl.net Thu May 23 08:25:15 2002 Received: from GWIA.HSC.WVU.EDU ([157.182.105.18]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4NCPF031378 for ; Thu, 23 May 2002 08:25:15 -0400 Received: from HSC-DOM5-Message_Server by GWIA.HSC.WVU.EDU with Novell_GroupWise; Thu, 23 May 2002 08:25:13 -0400 Message-Id: X-Mailer: Novell GroupWise Internet Agent 5.5.5.1 Date: Thu, 23 May 2002 08:24:47 -0400 From: "Peter Gannett" To: , Subject: Re: CCL:NBO_PLOTS Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Disposition: inline Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g4NCPF031379 You might try Grace (formerly xmgr). It runs under windows and other O/S systems (eg unix), is very robust. The link is: http://plasma-gate.weizmann.ac.il/Grace/ Pete Gannett >>> "temper" 05/22/02 09:24AM >>> Based on the NBO results (from GAUSSIAN 98W), Iam thinking to make plots. Does anybody know such kind of programs(freeware)? (The operating system is WINDOWS 2000). Thanks in advance. From chemistry-request@server.ccl.net Thu May 23 09:52:23 2002 Received: from mail.takas.lt ([212.59.31.78]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NDqM003522 for ; Thu, 23 May 2002 09:52:23 -0400 Received: from olegas ([212.59.29.37]) by mail.takas.lt with Microsoft SMTPSVC(5.0.2195.2966); Thu, 23 May 2002 15:52:16 +0200 Message-ID: <000c01c20261$c04d7460$251d3bd4@olegas> From: "Olegas Eicher-Lorka" To: Subject: BSSE Date: Thu, 23 May 2002 15:56:03 +0200 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0009_01C20272.57984740" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2600.0000 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 X-OriginalArrivalTime: 23 May 2002 13:52:16.0574 (UTC) FILETIME=[0C917DE0:01C20261] This is a multi-part message in MIME format. ------=_NextPart_000_0009_01C20272.57984740 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear all, In the "standard" BSSE equation (for a dimer AB): BSSE(AB) =3D E(AB)^AB - E(A)^A - E(B)^B + [E(A')^A - E(A')^AB + E(B)^B - = E(B)^AB] I've got most of the parameters, but how in G98W do I calculate E(A)^AB = and E(B)^AB, i.e. the energy of the monomer units in terms of the dimer = basis set. Thanks Olegas ------=_NextPart_000_0009_01C20272.57984740 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear all,
 
In the "standard" BSSE equation (for a = dimer=20 AB):
 
BSSE(AB) =3D E(AB)^AB - E(A)^A - E(B)^B = + [E(A')^A -=20 E(A')^AB + E(B)^B - E(B)^AB]
 
I've got most of the parameters, but = how in G98W do=20 I calculate E(A)^AB and E(B)^AB, i.e. the energy of the monomer units in = terms=20 of the dimer basis set.
 
Thanks
 
Olegas
------=_NextPart_000_0009_01C20272.57984740-- From chemistry-request@server.ccl.net Thu May 23 11:45:12 2002 Received: from hotmail.com ([64.4.23.103]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NFjB008896 for ; Thu, 23 May 2002 11:45:12 -0400 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 23 May 2002 08:45:06 -0700 Received: from 66.31.55.25 by lw15fd.law15.hotmail.msn.com with HTTP; Thu, 23 May 2002 15:45:06 GMT X-Originating-IP: [66.31.55.25] From: "Cameron Banks" To: chemistry@ccl.net Subject: Valence Shell Electron Pair Repulsion theory Date: Thu, 23 May 2002 11:45:06 -0400 Mime-Version: 1.0 Content-Type: text/plain; format=flowed Message-ID: X-OriginalArrivalTime: 23 May 2002 15:45:06.0511 (UTC) FILETIME=[CFC3E5F0:01C20270] Hello I am looking for code to perform Valence Shell Electron Pair Repulsion (VSEPR) theory calculations. I am not interested in web sites performing such calculation, rather standalone source code. Thanks Cameron. _________________________________________________________________ Join the world’s largest e-mail service with MSN Hotmail. http://www.hotmail.com From chemistry-request@server.ccl.net Thu May 23 08:57:22 2002 Received: from web12805.mail.yahoo.com ([216.136.174.40]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g4NCvL001062 for ; Thu, 23 May 2002 08:57:21 -0400 Message-ID: <20020523125720.66379.qmail@web12805.mail.yahoo.com> Received: from [64.94.101.217] by web12805.mail.yahoo.com via HTTP; Thu, 23 May 2002 05:57:20 PDT Date: Thu, 23 May 2002 05:57:20 -0700 (PDT) From: amor san juan Subject: benA.pdbq method preparation:AutoDock3 To: chemistry@ccl.net Cc: Ruth Huey MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii To all users of AutoDock3: You have also tested your ben.pdbq generated from your compiled AutoDock3. Your goal is to test the method you used to prepare the ligands prior using main programs autogrid & autodock. I am in that situation you had been before and Im thinking whether the benA.pdbq in file distribution file is derived by using ADT or autotors solely. By the way, what year that file example distibution from AutoDock3 had been made? Did Scripps made same file example distibution for AutoDock3.0, AutoDock3.0.5? Attention is being asked to AutoDock3 users. Please let me know how you were able to successfully justify that data coordinates you produced in ligands is logically correct as compared to the control benA.pdbq > from file example distribution. Your suggestions & expertise is highly appreciated. Amor San Juan __________________________________________________ Do You Yahoo!? LAUNCH - Your Yahoo! Music Experience http://launch.yahoo.com From chemistry-request@server.ccl.net Thu May 23 11:41:53 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NFfr008731 for ; Thu, 23 May 2002 11:41:53 -0400 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id LAA13956; Thu, 23 May 2002 11:41:53 -0400 (EDT) Sender: dwood@cornell.edu Message-ID: <3CED025A.53E488B7@cornell.edu> Date: Thu, 23 May 2002 10:53:15 -0400 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Xenon vdw parameters Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all Does anyone out there know (or where I can find) CHARMM van der Waals parameters for Xenon? My par_all22_all.inp file has parameters for He and Ne, but no Xe. Thanks in advance, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu May 23 10:53:25 2002 Received: from georgetown.edu ([141.161.1.110]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NErP006641 for ; Thu, 23 May 2002 10:53:25 -0400 Received: from mailhost.georgetown.edu (mailhost.georgetown.edu [141.161.1.103]) by georgetown.edu (8.12.2/8.12.2) with ESMTP id g4NErMmb021982 for ; Thu, 23 May 2002 10:53:22 -0400 (EDT) Received: from czar (wkstn206-243.nrb.georgetown.edu [141.161.206.243]) (user=pap4 mech=LOGIN bits=0) by mailhost.georgetown.edu (8.12.2/8.12.2) with ESMTP id g4NErLP6022095 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Thu, 23 May 2002 10:53:22 -0400 (EDT) From: "Pavel A. Petukhov" To: Subject: movie of docking Date: Thu, 23 May 2002 10:56:31 -0400 Message-ID: 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 IMO, Build 9.0.2416 (9.0.2910.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal Is there any way to visualize the docking trajectory of a ligand to the binding site starting from a distance of about 10 ang? The idea is to show how the ligand moves toward the binding site, how it adjusts its orientation when bumps on other atoms, and how it finally sticks to the binding site. Pavel A. Petukhov Drug Discovery Group Georgetown University Medical Center New Research Building EP15 3900 Reservoir Road NW Washington, DC 20007-2197 day-phone: 202-687-2368 fax: 202-687-0738 Email: pap4@georgetown.edu From chemistry-request@server.ccl.net Thu May 23 10:54:54 2002 Received: from sd.accelrys.com ([146.202.0.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NEsr006718 for ; Thu, 23 May 2002 10:54:54 -0400 Received: (from jnauss@localhost) by sd.accelrys.com (8.11.0/8.11.0) id g4NErbZ19792 for chemistry@ccl.net; Thu, 23 May 2002 07:53:38 -0700 From: Jeffrey Nauss Received: from sandmail01.sd.accelrys.com (sandmail01.sd.accelrys.com [172.30.160.90]) by sd.accelrys.com (8.11.0/8.11.0) with ESMTP id g4NEra719779 for ; Thu, 23 May 2002 07:53:36 -0700 To: chemistry@ccl.net Subject: Accelrys CHARMm and InsightII workshops in North Carolina MIME-Version: 1.0 X-Mailer: Lotus Notes Release 5.0.9a January 7, 2002 Message-ID: Date: Thu, 23 May 2002 07:54:41 -0700 X-MIMETrack: Serialize by Router on sandmail01/Server/Accelrys(Release 5.0.9 |November 16, 2001) at 05/23/2002 07:54:45 AM, Serialize complete at 05/23/2002 07:54:45 AM 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 g4NEss006721 Accelrys Inc. will be holding a pair of two-day workshops at the North Carolina Supercomputing Center, Research Triangle Park, NC, in June 2002. On June 25-26, the "CHARMm Workshop" will be offered. This workshop will provide an in-depth coverage of molecular mechanics and dynamics focusing on the use of CHARMm. Applications of CHARMm will also be presented. Both command line usage as well as use in InsightII will be covered. No experience is necessary but knowledge of InsightII will be helpful. On June 27-28, the workshop "Structure-Based Drug Design with InsightII" will be conducted. This workshop is for experienced users of InsightII who are interested in docking and drug design. The focus will be on detailed studies of single ligand interactions with specific receptors. Topics will include binding site identification, conformational searches, and analysis of protein-ligand complexes. Extensive experience or completion of the "Introduction to Life Science Modeling with InsightII" workshop is required. Fees for each 2-day course are $1200 commercial, $900 government, and $660 academic. Registration is on-line at URL http://www.accelrys.com/training/macro/registration.php. Further detailed information about this and other Accelrys training workshops can be found at the Accelrys website (http://www.accelrys.com/training/macro/schedule.html). Please do not hesitate to contact me should you have any questions. Thank you very much. Jeffrey L. Nauss 858-799-5555 -- Jeffrey L. Nauss, Ph.D. Manager US Training, Global Bioinformatics and Macromolecular Modeling Training Accelrys Inc. 9685 Scranton Road San Diego, CA 92121-3752 Phone: 858-799-5555 Fax: 858-799-5100 E-mail: jnauss@accelrys.com http://www.accelrys.com/training From chemistry-request@server.ccl.net Thu May 23 16:00:13 2002 Received: from ns-0.mssm.edu ([146.203.100.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NK0D019613 for ; Thu, 23 May 2002 16:00:13 -0400 Received: from CONVERSION-DAEMON.ns-0.mssm.edu by ns-0.mssm.edu (PMDF V6.1 #38773) id <0GWK00E01Y87LQ@ns-0.mssm.edu> for chemistry@ccl.net; Thu, 23 May 2002 16:00:07 -0400 (EDT) Received: from ROTATEGX400 ([146.203.3.181]) by ns-0.mssm.edu (PMDF V6.1 #38773) with SMTP id <0GWK00DCAY86LW@ns-0.mssm.edu> for chemistry@ccl.net; Thu, 23 May 2002 16:00:07 -0400 (EDT) Date: Thu, 23 May 2002 16:02:15 -0400 From: Joshua Speidel Subject: CHARMM Crystal problems... To: chemistry@ccl.net Message-id: MIME-version: 1.0 X-MIMEOLE: Produced By Microsoft MimeOLE V5.50.4910.0300 X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) Content-type: text/plain; charset=iso-8859-1 Content-transfer-encoding: 7bit Importance: Normal X-Priority: 3 (Normal) X-MSMail-priority: Normal Hello, I am trying to set up a PME molecular dynamics system, and have been having trouble getting past the crystal build command. I'm trying to use a hexagonal box. After I've read in coordinates, topology etc., I use these commands to build the crystal: CRYSTAL DEFINE HEXA 72.0 72.0 27.0 90.0 90.0 120.0 CRYSTAL BUILD CUTOFF 12.5 NOPER 5 (-Y,X-Y,Z) (-X+Y,-X,Z) (-X,-Y,Z) (Y,-X+Y,Z) (X-Y,X,Z) OPEN WRITE UNIT 9 CARD NAME "./hexa12.5.xtl" CRYSTAL WRITE UNIT 9 CARD ... This part appears to work fine, but should I be concerned about the message 'THERE ARE ROTATIONS FOR THIS TRANSFORMATION SET' that I get at the end of the transformations? How do I / Should I include these when I go on > from here? Also, the operations that I included are for a P6 hexagonal prism, but I saw in the test files provided with charmm that when they test the different kinds of crystals they don't use operations. Should I be using them? In my next step, I simply try to calculate the energy. Using the same input file I deleted last two lines 'OPEN WRITE ...' and 'CRYSTAL WRITE ...' and added a line that simply says 'ENERGY' In the output, it starts CHARMM> energy : updating the image atom lists and remapping ...and then it says ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW even though my sysem has only 3200 residues and 11000 atoms. I'm not sure what is happening. I feel that the inability to calculate the energy is related to my questions about the crystal, but I'm not sure. Comments on any part of this long email are greatly appreciated. Thank you, Josh ps. This is less critical, so I put it at the end, but while trying to make the hexa.xlt file, I found that CUTOFF 15 and CUTOFF 16 caused the program to crash, but that a CUTOFF of 12.5, 14.5, and 20 worked okay (as far as I could tell). I'm really curious as to why this is. Any thoughts? Thanks! --- Joshua Speidel Graduate Student Mount Sinai School of Medicine New York, NY 10029 From chemistry-request@server.ccl.net Thu May 23 15:51:45 2002 Received: from mr.usu.edu ([129.123.1.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4NJpj019308 for ; Thu, 23 May 2002 15:51:45 -0400 Received: from pc3 (pc3.chem.usu.edu [129.123.3.37]) by mr.usu.edu (Postfix) with SMTP id 4BB2C1D43C for ; Thu, 23 May 2002 13:51:46 -0600 (MDT) Reply-To: From: "Tapas Kar" To: Subject: MNDO Raman Spectra Date: Thu, 23 May 2002 13:49:40 -0600 Message-ID: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0014_01C20260.AF9DDE30" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MIMEOLE: Produced By Microsoft MimeOLE V6.00.2600.0000 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_0014_01C20260.AF9DDE30 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit Dear CClers, Could any one tell me if there are free softwares available for doing IR, Raman, XPS, NMR etc spectra using MNDO/PM3/AM1 theories. Tapas *********************************************** "We owe a lot to the Indians, who taught us how to count, without which no worthwhile scientific discovery could have been made." - Albert Einstein - "The value of pi was first calculated by Budhayana, and he explained the concept of what is now known as the Pythagorean Theorem. British scholars have last year (1999) officially published that Budhayan’s works dates to the 6th Century, which is long before the European mathematicians." ---------------------------------------------------------------------------- ---- Tapas Kar, Ph. D Department of Chemistry & Biochemistry Utah State University Logan, UT 84322-0300 Tel: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu Web:http://www.chem.usu.edu/faculty/Tapas/index.html ------=_NextPart_000_0014_01C20260.AF9DDE30 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

Dear CClers,

 Could any one tell me if = there are=20 free softwares available for doing

 IR,=20 Raman, XPS, NMR etc spectra using MNDO/PM3/AM1 = theories.

Tapas

***********************************************
"We owe a lot to the Indians, who taught = us how to=20 count, without
which no worthwhile scientific discovery could have = been=20 made."
         &n= bsp;           &nb= sp;           &nbs= p;        =20 - Albert Einstein -
"The value = of pi was=20 first calculated by Budhayana, and he explained
the concept of what = is now=20 known as the Pythagorean Theorem. British
scholars have last year = (1999)=20 officially published that Budhayan=92s
works dates to the 6th = Century, which is=20 long before the=20 European
mathematicians."
----------------------------------= ----------------------------------------------
Tapas=20 Kar, Ph. D
Department of Chemistry & Biochemistry
Utah State=20 University
Logan, UT 84322-0300

Tel: 435-797-7230
Fax:=20 435-797-3390
Email: tapaskar@cc.usu.edu
Web:http://www.chem.usu.edu/faculty/Tapas/index.html

 
------=_NextPart_000_0014_01C20260.AF9DDE30-- From chemistry-request@server.ccl.net Thu May 23 20:24:44 2002 Received: from mercury.sunesis.com ([64.240.200.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g4O0Oi004853 for ; Thu, 23 May 2002 20:24:44 -0400 X-MimeOLE: Produced By Microsoft Exchange V6.0.5762.3 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: RE: movie of docking Date: Thu, 23 May 2002 17:24:38 -0700 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: movie of docking Thread-Index: AcICrUF9LbE3o59XSyqLwzlmVabCjAABAAcQ From: "DeLano, Warren" To: "Pavel A. Petukhov" , Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id g4O0Oi004854 PyMOL can do this. http://www.pymol.org Basic idea: 1. load the ligand and protein as separate objects load prot.pdb load lig.pdb 2. define a movie of a certain length mset 1 x10 (here, a 10 frame example, but you could define 100's or 1000's) 3. in the first frame of the movie, displace the ligand from the active site mdo 1: reset object=lig; translate [9,0,0],object=lig (9 A displacement, along X-axis...) 4. in the remaining 9 frames of the movie, move the ligand back incrementally. mdo 2: translate [-1,0,0],object=lig mdo 3: translate [-1,0,0],object=lig mdo 4: translate [-1,0,0],object=lig mdo 5: translate [-1,0,0],object=lig mdo 6: translate [-1,0,0],object=lig mdo 7: translate [-1,0,0],object=lig mdo 8: translate [-1,0,0],object=lig mdo 9: translate [-1,0,0],object=lig Now you can view the movie in real time (hit play), write it out as a series of ray-traced frames with lighting and shadows, experiment with various representations, and so on. With more work, you could use more frames (more smooth), include rotations, use the sculpting engine to simulate VDW collisions, or write the whole thing as a Python program, instead of merely a PyMOL script. Alternatively, you could create the trajectory using an MD/Mechanics package and just read the frames into PyMOL for viewing and rendering. Cheers, Warren PS. PyMOL momentum continues to build! Several large pharma and biotech companies have now lent their support to this unrestricted open-source viewer, builder, and animation tool. Please consider participating if you would like to nuture a solid alternative to the closed-source commercial offerings for desktop visualization : ). -- mailto:warren@delanoscientific.com Warren L. DeLano, Ph.D. > -----Original Message----- > From: Pavel A. Petukhov [mailto:pap4@georgetown.edu] > Sent: Thursday, May 23, 2002 7:57 AM > To: chemistry@ccl.net > Subject: CCL:movie of docking > > > Is there any way to visualize the docking trajectory of > a ligand to the binding site starting from a distance of > about 10 ang? The idea is to show how the ligand moves > toward the binding site, how it adjusts its orientation when > bumps on other atoms, and how it finally sticks to the > binding site. > > Pavel A. Petukhov > Drug Discovery Group > Georgetown University Medical Center > New Research Building EP15 > 3900 Reservoir Road NW > Washington, DC 20007-2197 > day-phone: 202-687-2368 > fax: 202-687-0738 > Email: pap4@georgetown.edu > > -= 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 > > > > > >