From chemistry-request@ccl.net Tue Jan 6 14:13:37 2004 Received: from mail.ic.sunysb.edu (mail.ic.sunysb.edu [129.49.1.4]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i06JD6X9006438 for ; Tue, 6 Jan 2004 14:13:06 -0500 Received: from postal.ic.sunysb.edu (mail [129.49.1.4]) by mail.ic.sunysb.edu (8.12.10/8.12.10) with SMTP id i06JCnLc016941; Tue, 6 Jan 2004 14:13:06 -0500 (EST) Received: from smtp.ic.sunysb.edu ([129.49.1.24]) by postal.ic.sunysb.edu (SAVSMTP 3.1.1.32) with SMTP id M2004010614130500324 ; Tue, 06 Jan 2004 14:13:05 -0500 Received: from sparky.ic.sunysb.edu (daemon-.at.-sparky.ic.sunysb.edu [129.49.1.3]) by smtp.ic.sunysb.edu (8.12.10/8.12.10) with ESMTP id i06JD6RM017061; Tue, 6 Jan 2004 14:13:06 -0500 (EST) Received: from localhost (yonyang@localhost) by sparky.ic.sunysb.edu (8.12.10/8.12.9) with ESMTP id i06JD5PA021429; Tue, 6 Jan 2004 14:13:05 -0500 (EST) Date: Tue, 6 Jan 2004 14:13:05 -0500 (EST) From: Yong Liang Yang To: chemistry-.at.-ccl.net cc: yonyang-.at.-ic.sunysb.edu Subject: Internal Coordinate Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear CCL users: Happy new year! A simple question, how can I convert other coordinate data into internal coordinate data, (especially, create internal coordinate input files for AMSOL or AMPAC calculation). And how can I visualize the internal coordinate results from AMSOL or AMPAC? Any suggestions are appreciated! Cheers Yong.L.Y. Dept. of Chemistry (o) 631-632-5796 From chemistry-request@ccl.net Tue Jan 6 22:25:57 2004 Received: from cmsrelay03.mx.net (cmsrelay03.mx.net [165.212.11.112]) by server.ccl.net (8.12.8/8.12.8) with SMTP id i073PPX9011247 for ; Tue, 6 Jan 2004 22:25:26 -0500 Received: from uadvg137.cms.usa.net (165.212.11.137) by cmsoutbound.mx.net with SMTP; 7 Jan 2004 03:25:25 -0000 Received: from uwdvg018.cms.usa.net [165.212.8.18] by uadvg137.cms.usa.net (ASMTP/) via mtad (C8.MAIN.3.11E) with ESMTP id 432iagDZX0359M37; Wed, 07 Jan 2004 03:25:23 GMT X-USANET-Auth: 165.212.8.18 AUTO david.w.miller.-at-.stanfordalumni.org uwdvg018.cms.usa.net Received: from 216.84.163.209 [216.84.163.209] by uwdvg018.cms.usa.net (USANET web-mailer CM.0402.7.03); Wed, 07 Jan 2004 03:25:22 -0000 Date: Wed, 07 Jan 2004 03:25:22 -0000 From: David Miller To: Subject: CCL: ChemTK and large data sets X-Mailer: USANET web-mailer (CM.0402.7.03) Mime-Version: 1.0 Message-ID: <393iagDZw9424S18.1073445922.-at-.uwdvg018.cms.usa.net> Content-Type: text/plain; charset=ISO-8859-1 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id i073PvX9011257 ChemTK version 2.9 is now available for download from: http://www.sageinformatics.com Among other new features, ChemTK 2.9 now runs in a "virtual mode" designed to reduce memory usage. Using the Aug 2000 release of the NCI Open Database as a test case, the new version requires an average of only 75 MB of memory for every 100,000 molecules opened. Other features include: - Document limit increased to 1,000,000 molecules - Hierarchical sorting added (e.g., secondary and tertiary sorting) - The R Table View supports substructure and name searches, clipboard operations, depiction enlargement, column insertion and deletion, and expanded export options Best Regards, David W. Miller, Ph.D. Sage Informatics LLC dmiller.-at-.sageinformatics.com ____________________________________________________________________ From chemistry-request@ccl.net Wed Jan 7 08:24:29 2004 Received: from postbode01.zonnet.nl (postbode01.zonnet.nl [62.58.50.88]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i07DNvX9029991 for ; Wed, 7 Jan 2004 08:23:58 -0500 Received: (qmail 2860 invoked by uid 10); 7 Jan 2004 13:23:56 -0000 Received: (vexira-qq 02851-6F3EE432 invoked from network) 07 Jan 2004 14:23:55 +0100 Received: from unknown (HELO chem.vu.nl) ([62.59.65.24]) (envelope-sender ) by postbode01.zonnet.nl (qmail-ldap-1.03) with SMTP for < >; 7 Jan 2004 13:23:55 -0000 Message-ID: <3FFBE795.4050106.-at-.chem.vu.nl> Date: Wed, 07 Jan 2004 12:03:49 +0100 From: Anton Feenstra Reply-To: feenstra.-at-.chem.vu.nl User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Rick Venable CC: Wei Shi , chemistry.-at-.ccl.net Subject: Re: CCL:CCL References: In-Reply-To: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-AntiVirus: checked by Vexira MailArmor (version: 2.0.1.16; VAE: 6.23.0.2; VDF: 6.23.0.22; host: postbode01.zonnet.nl) X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Rick Venable wrote: > For a solvated protein simulation, I'd monitor the potential energy, the > radius of gyration, and the bacbone RMSD relative to the starting > structure. When all 3 of these become flat, one could argue that > the system is equilibrated; this could require 100s of picoseconds. Although indeed one can argue this, it is hard to tell what 'flat' means in a practical sense. For a seond-year lecture I give I have three slides each giving the rmsd of a protein w/r to the x-ray structure. All three of them level off to a nice plateau at the end, and appear to be genuinly equilibrated in the way you define that. But, the three plots are of the same simulation, the first of 0-100ps, the second of 0-1ns, and the last of 0-10ns! If you overlay them, they are almost the same, except for the scale of the axes! Those of you who'd like to see them, please ask me and I can send you the three jpg files (~50k each). While I don't regularly monitor r_gyr or e_pot, I don't know but suspect that they would show similar behaviour... (although they may equilibrate much faster than the rmsd). -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra.-at-.chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Tue Jan 6 03:20:10 2004 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i068JcX9022639 for ; Tue, 6 Jan 2004 03:19:39 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AdmR8-000NGFC; Tue, 6 Jan 2004 09:19 +0100 Message-ID: <3FFA5CFB.4050703{at}chem.vu.nl> Date: Tue, 06 Jan 2004 08:00:11 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: Sivanesan Dakshanamurthy CC: chemistry{at}ccl.net Subject: Re: CCL:calculate chi angle, surface area References: <187835185658.185658187835{at}imap.georgetown.edu> In-Reply-To: <187835185658.185658187835{at}imap.georgetown.edu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Sivanesan Dakshanamurthy wrote: > Dear All: > > I looking for a program to calculate the following: > > surface area of a protein, 'chi' angle of a given sidechain, to generate 3D graph of a given data apart from excel. There are such tools in the Gromacs MD package, which can be downloaded for free at www.gromacs.org. Look for g_chi, g_sas, and g_sgangle. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra{at}chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Wed Jan 7 14:26:39 2004 Received: from kafka.net.nih.gov (mailfwd.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i07JQ7X9022674 for ; Wed, 7 Jan 2004 14:26:08 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.10/8.12.9) with ESMTP id i07JQ8cD017434; Wed, 7 Jan 2004 14:26:08 -0500 (EST) Date: Wed, 7 Jan 2004 14:14:59 -0500 From: Rick Venable To: Anton Feenstra cc: Wei Shi , chemistry)at(ccl.net Subject: Re: CCL:CCL In-Reply-To: <3FFBE795.4050106)at(chem.vu.nl> Message-ID: References: <3FFBE795.4050106)at(chem.vu.nl> ReplyTo: Rick_Venable)at(nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_NJABL,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) You make my points clearly-- don't use just one probe to define equilibration, and it may require longer simulation times than 10-50 ps to achieve equilibration. The timescale plots are interesting, but I do wonder about such a large change in backbone RMSD; over 40 A suggests quite a large change from the xtal coords. What were the simulation conditions for this? Is the "equilibrated" structure obtained at long times significant, i.e. is there any evidence to indicate agreement with epxt data? > Rick Venable wrote: > > For a solvated protein simulation, I'd monitor the potential energy, the > > radius of gyration, and the bacbone RMSD relative to the starting > > structure. When all 3 of these become flat, one could argue that > > the system is equilibrated; this could require 100s of picoseconds. On Wed, 7 Jan 2004, Anton Feenstra wrote: > Although indeed one can argue this, it is hard to tell what 'flat' > means in a practical sense. For a seond-year lecture I give I have > three slides each giving the rmsd of a protein w/r to the x-ray > structure. All three of them level off to a nice plateau at the end, > and appear to be genuinly equilibrated in the way you define that. > But, the three plots are of the same simulation, the first of 0-100ps, > the second of 0-1ns, and the last of 0-10ns! If you overlay them, they > are almost the same, except for the scale of the axes! Those of you > who'd like to see them, please ask me and I can send you the three jpg > files (~50k each). > > While I don't regularly monitor r_gyr or e_pot, I don't know but > suspect that they would show similar behaviour... (although they may > equilibrate much faster than the rmsd). =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable)at(nih.gov ALT email: rvenable)at(speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=