From chemistry-request@ccl.net Fri Jul 9 11:31:06 2004 Received: from glaurung.gpcc.itd.umich.edu (glaurung.gpcc.itd.umich.edu [141.211.2.181]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69GV5UW006930 for ; Fri, 9 Jul 2004 11:31:05 -0500 Received: from asteroids.gpcc.itd.umich.edu (asteroids.gpcc.itd.umich.edu [141.211.2.218]) by glaurung.gpcc.itd.umich.edu (8.9.3p2/4.3-mailhub) with ESMTP id MAA16417; Fri, 9 Jul 2004 12:36:52 -0400 (EDT) Received: from localhost (weishi@localhost) by asteroids.gpcc.itd.umich.edu (8.9.3p2/5.1-client) with ESMTP id MAA09679; Fri, 9 Jul 2004 12:36:52 -0400 (EDT) Precedence: first-class Date: Fri, 9 Jul 2004 12:36:52 -0400 (EDT) From: Wei Shi X-X-Sender: weishi|at|asteroids.gpcc.itd.umich.edu To: Rick Venable cc: chemistry|at|ccl.net Subject: Re: CCL:protein cross the boundary of the box in PBC In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, Rick, Would you mind I ask you a question about the relationship between 1-4 interaction and the NPHI, the number of dihedrals in the psf file? I have a very simple peptide system composed of 5 residues without using periodic boundary condition. From the psf file, I know that 210 !NPHI. I check that all the 210 dihidrals in the psf file are unique, i.e, their is no case like A-B-C-D, and A-e-f-D, or D-g-h-A in the dihedral part. Here, I use A, B, C, and D to denote the number of atoms, like 12 14 17 19 in the dihedral part of the psf file, etc. Hence, I think the number of 1-4 interactions should be equal to 210 when the nonbonded interaction is calculated. However, from the output of CHARMm, it says "with mode 5 found 230 exclusions and 205 interactions(1-4)". Obviously, 205 is less than 210. What is wrong with my thought? By the way, if I use the periodic boundary condition, what does that mean for 1-4 interaction? For eample, if I have A-B-C-D in the primary box and A'-B'-C'-D' in one of the image cells, how the 1-4 interaction is calculated if distance of AD' is less than AD? I think, in this case, CHARMm will neglect AD interaction, but consider AD' interaction. If AD' is calculated, CHARMm use 1-4 VDW parameters or other VDW parameters? I am sorry to ask you this question. I have posted this question in the CHARMm bbs but without reply. Thanks very much for your help, Wei Shi From chemistry-request@ccl.net Fri Jul 9 01:29:53 2004 Received: from mail.kemi.dtu.dk (mail.kemi.dtu.dk [130.225.67.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i696Tpjc021527 for ; Fri, 9 Jul 2004 01:29:52 -0500 Received: from [192.38.70.75] (pon.ok.dtu.dk [192.38.70.75]) by mail.kemi.dtu.dk (8.11.6/8.11.6) with ESMTP id i696ZWP03326; Fri, 9 Jul 2004 08:35:32 +0200 Mime-Version: 1.0 X-Sender: pon(at)mail.kemi.dtu.dk Message-Id: In-Reply-To: <40ED7448.10107(at)trentu.cA> References: <40ED7448.10107(at)trentu.cA> Date: Fri, 9 Jul 2004 08:37:11 +0200 To: Errol Lewars From: Per-Ola Norrby Subject: Re: CCL:conformers and rate Cc: chemistry(at)ccl.net Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net >2004 July 8 > >The rate of formation of products Pa and Pb from quickly interconverting >conformers Ca and Cb is treated with the the Curtin/Hammett and >Winstein-Holness equations (the Curtin-Hammett principle, in particular, >is well-known): J. I Seeman, Chem Rev, 1983, 83, 83; E. L. Eliel, "From >Cologne to Chapel Hill", ACS, 1990, pp. 31-33. > >Question: has anyone a reference to a discussion of the case of rapidly >interconverting conformers Ca and Cb, where Ca, although the minor >conformer, is the only one that can react with X to form a product CaX, >through transition state Ta; intuition aside, has someone explicitly >addressed whether the _experimental_ activation E is measuring the Ta-Ca >energy difference, or the Ta-Cb difference? Provided that the interconversion is fast relative to the final reaction, the free energy of activation should be relative to the ensemble energy (which is slightly lower than the lowest of Ca and Cb). The apparent activation energy is taken from an expression where you consider the total concentration of reactant. The sole effect of the pre-equilibrium is to make the effective concentration lower, with a concominant lowering of the rate which corresponds exactly to the free energy difference between the reacting conformer and the free energy of the ensemble. You can get the latter by assuming a virtual species corresponding to the total concentration of the reagent, and use the standard Boltzmann expression. The above wasn't perfectly clear (I haven't digested my coffee yet), but it should be correct. The math is available in the Ph.D. Thesis of Torben Rasmussen (Copenhagen 2001), and he took much of it from H Maskil, "The Physical Basis of Organic Chemistry", Oxford 1985. /Per-Ola -- Per-Ola Norrby, Assoc. Professor, http://organisk.kemi.dtu.dk/PON/ Technical University of Denmark, Department of Chemistry Building 201, Kemitorvet, DK-2800 Kgs. Lyngby, Denmark Email: pon(at)kemi.dtu.dk tel +45-45252123, fax +45-45933968 From chemistry-request@ccl.net Fri Jul 9 01:58:58 2004 Received: from exmails1.chem.ucla.edu (exmails1.chem.ucla.edu [169.232.134.2]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i696wujc022118 for ; Fri, 9 Jul 2004 01:58:57 -0500 Received: from [169.232.128.32] (dial32.chem.ucla.edu [169.232.128.32]) (authenticated bits=0) by exmails1.chem.ucla.edu (8.12.8/8.12.8) with ESMTP id i6974aEb029977; Fri, 9 Jul 2004 00:04:42 -0700 Mime-Version: 1.0 X-Sender: scerri*at*chlorine.chem.ucla.edu (Unverified) Message-Id: Date: Thu, 8 Jul 2004 23:59:33 -0700 To: ccl From: Eric Scerri Subject: Question on molecular structure and QM Content-Type: text/plain; charset="us-ascii" ; format="flowed" X-Spam-Status: No, hits=0.3 required=7.5 tests=FVGT_s_OBFU_Q1 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net The following is a somewhat general philosophical question. I would very much appreciate the comments of computational chemists. In the philosophy of chemistry literature much has been made of the fact that molecular structure cannot be strictly deduced from QM. I am referring to the work of Guy Wooley in the UK and Hans Primas at the ETH. The basis of this claim is that structure comes after applying the Born-Oppenheimer approximation to fix the nuclei. These authors claim that in this sense molecular structure has not been "reduced" to QM. They point to the fact that the Hamiltonians for two isomers of an organic compound, for example, are identical in the absence of the B-O approximation and they conclude that a strictly QM calculation cannot therefore distinguish between the two structures in question. I would be happy to pull some references together for anyone interested in studying the original articles. But I just wanted to hear some general reactions to such claims. -- Dr. Eric Scerri , UCLA, Department of Chemistry & Biochemistry, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 USA E-mail : scerri*at*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@ccl.net Fri Jul 9 13:54:45 2004 Received: from ntmms01.chla.usc.edu (chl179129.usc.edu [128.125.179.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69IsiUW009828 for ; Fri, 9 Jul 2004 13:54:44 -0500 Received: from 10.3.1.165 by ntmms01.chla.usc.edu with ESMTP (CHLA SMTP Relay (MMS v5.6.0)); Fri, 09 Jul 2004 12:00:32 -0700 X-Server-Uuid: 3F66CE27-8E7A-45D4-9872-50BC1A7F95DE Received: by ntsmtp01.chla.usc.edu with Internet Mail Service ( 5.5.2653.19) id <32BZWJS3>; Fri, 9 Jul 2004 12:00:31 -0700 Message-ID: <73564B8DE398D61180500008C75D7E49033E5FE4@NTMAIL03> From: "Pandey, Jaya" To: "'chemistry-.at.-ccl.net'" Subject: Docking tool Date: Fri, 9 Jul 2004 12:00:28 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 6CF034DA1ZC98219-01-01 Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear All, Does anyone know of a efficient docking freeware that can be used for a rapid drug screening library. I am using AutoDock currently but unfortunately I am not very comfortable with it for a rapid screen. Any clues?? Thanks Jaya From chemistry-request@ccl.net Fri Jul 9 04:47:24 2004 Received: from mail1.hku.hk (mail1.hku.hk [147.8.2.98]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i699lLjc027242 for ; Fri, 9 Jul 2004 04:47:22 -0500 Received: from localhost (webmail01.hku.hk [147.8.2.175]) by mail1.hku.hk (8.12.8p1-030919/8.12.8) with ESMTP id i699qaF8028596 for ; Fri, 9 Jul 2004 17:52:37 +0800 (CST) Received: from tonegawa.hku.hk (tonegawa.hku.hk [147.8.148.93]) by imp.webmail.hku.hk (IMP) with HTTP for ; Fri, 9 Jul 2004 17:55:08 +0800 Message-ID: <1089366908.40ee6b7c24f87-.at.-imp.webmail.hku.hk> Date: Fri, 9 Jul 2004 17:55:08 +0800 From: h9807907-.at.-hkusua.hku.hk To: CHEMISTRY-.at.-ccl.net Subject: Questions about CHARMM I/O MIME-Version: 1.0 Content-Type: text/plain; charset=Big5 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 147.8.148.93 X-MailScanner: 0 X-Spam-Status: No, hits=2.5 required=7.5 tests=FROM_ENDS_IN_NUMS,NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Dear all, I am new to CHARMM and I hope that you can give me some ideas of the following questions. 1) Do anyone know how to print out the coordinate file and restart file at different time intervals during a MD similation? Is that possible by modifying the .inp file? 2) How can I suppress the print of those files, such as .vel .ene, which I cannot read? Thanks for you help in advance. Regards Larry From chemistry-request@ccl.net Fri Jul 9 13:53:04 2004 Received: from ntmms01.chla.usc.edu (chl179129.usc.edu [128.125.179.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69Ir2UW009747 for ; Fri, 9 Jul 2004 13:53:03 -0500 Received: from 10.3.1.165 by ntmms01.chla.usc.edu with ESMTP (CHLA SMTP Relay (MMS v5.6.0)); Fri, 09 Jul 2004 11:58:29 -0700 X-Server-Uuid: 3F66CE27-8E7A-45D4-9872-50BC1A7F95DE Received: by ntsmtp01.chla.usc.edu with Internet Mail Service ( 5.5.2653.19) id <32BZWJR4>; Fri, 9 Jul 2004 11:58:28 -0700 Message-ID: <73564B8DE398D61180500008C75D7E49033E5FE3@NTMAIL03> From: "Pandey, Jaya" To: "'chemistry-.at.-ccl.net'" Subject: 3-D Structure file for Inosine molecule Date: Fri, 9 Jul 2004 11:58:27 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 6CF0355F1ZC98137-01-01 Content-Type: text/plain Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hi, Can someone provide me with the 3-D structure file(.pdb format) for my studies? I will be thankful for it. Jaya From chemistry-request@ccl.net Fri Jul 9 17:19:29 2004 Received: from ntmms01.chla.usc.edu (chl179129.usc.edu [128.125.179.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69MJSga015209 for ; Fri, 9 Jul 2004 17:19:28 -0500 Received: from 10.3.1.165 by ntmms01.chla.usc.edu with ESMTP (CHLA SMTP Relay (MMS v5.6.0)); Fri, 09 Jul 2004 15:25:04 -0700 X-Server-Uuid: 3F66CE27-8E7A-45D4-9872-50BC1A7F95DE Received: by ntsmtp01.chla.usc.edu with Internet Mail Service ( 5.5.2653.19) id <32BZWLKM>; Fri, 9 Jul 2004 15:25:03 -0700 Message-ID: <73564B8DE398D61180500008C75D7E49033E5FE9@NTMAIL03> From: "Pandey, Jaya" To: "'Carsten Detering '" cc: "'chemistry$at$ccl.net'" Subject: RE: ADL: VLS using AutoDock Date: Fri, 9 Jul 2004 15:25:01 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 6CF1C4CA1ZC102444-01-01 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Carsten, Thanks a lot!! Jaya -----Original Message----- From: Carsten Detering To: Pandey, Jaya Sent: 7/9/04 2:30 PM Subject: Re: ADL: VLS using AutoDock it is free for academics. you have to contact them and then fill in a license agreement. they dont support the academic verison, but the documentation is not too bad. Pandey, Jaya wrote: > Hi Carsten > > I was checking the website, seems the docking tool is not a freeware and the > prices are quite high for me to think about. If you have any ways to get it > free please let me know. > > Thanks > > Jaya > > -----Original Message----- > From: Carsten Detering > To: Pandey, Jaya > Sent: 7/9/04 1:11 PM > Subject: Re: ADL: VLS using AutoDock > > Pandey, > > you can use a foreach loop to dock a library. Just write out every > ligand in a single mol2/pdbq file, and setup a gpf file that contains > every ligand atom type. Then use the foreach loop to create a dpf file > for every ligand, which in turn you can dock using the foreach loop > again. > Concerning your other question in the CCl: > If you are in an academic setting, check out openeye software > (www.eyesopen.com). THey have a very fast docking machine. > > Hope this helps. > > Carsten > > Pandey, Jaya wrote: > > >>Dear All, >> >>Can someone help me to understand if there is any possibility of > > loading the > >>whole library of small molecules and use the AutoDock for screening. > > Any > >>help is appreciated. >> >>Thanks >> >> >>Jaya >> >>________________________________________________ >>--- ADL: AutoDock List --- > > http://www.scripps.edu/pub/olson-web/doc/autodock/ --- > From chemistry-request@ccl.net Fri Jul 9 16:16:43 2004 Received: from ntmms01.chla.usc.edu (chl179129.usc.edu [128.125.179.129]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69LGfga014145 for ; Fri, 9 Jul 2004 16:16:42 -0500 Received: from 10.3.1.165 by ntmms01.chla.usc.edu with ESMTP (CHLA SMTP Relay (MMS v5.6.0)); Fri, 09 Jul 2004 14:22:21 -0700 X-Server-Uuid: 3F66CE27-8E7A-45D4-9872-50BC1A7F95DE Received: by ntsmtp01.chla.usc.edu with Internet Mail Service ( 5.5.2653.19) id <32BZWKZP>; Fri, 9 Jul 2004 14:22:20 -0700 Message-ID: <73564B8DE398D61180500008C75D7E49033E5FE7@NTMAIL03> From: "Pandey, Jaya" To: "'Carsten Detering '" cc: "'chemistry)at(ccl.net'" Subject: RE: ADL: VLS using AutoDock Date: Fri, 9 Jul 2004 14:21:39 -0700 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) X-WSS-ID: 6CF1D3071ZC101255-01-01 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Carsten, I appreciate your quick repsonse. I will try it and get back to you in case of any difficulty. Thanks again, Jaya -----Original Message----- From: Carsten Detering To: Pandey, Jaya Sent: 7/9/04 1:11 PM Subject: Re: ADL: VLS using AutoDock Pandey, you can use a foreach loop to dock a library. Just write out every ligand in a single mol2/pdbq file, and setup a gpf file that contains every ligand atom type. Then use the foreach loop to create a dpf file for every ligand, which in turn you can dock using the foreach loop again. Concerning your other question in the CCl: If you are in an academic setting, check out openeye software (www.eyesopen.com). THey have a very fast docking machine. Hope this helps. Carsten Pandey, Jaya wrote: > Dear All, > > Can someone help me to understand if there is any possibility of loading the > whole library of small molecules and use the AutoDock for screening. Any > help is appreciated. > > Thanks > > > Jaya > > ________________________________________________ > --- ADL: AutoDock List --- http://www.scripps.edu/pub/olson-web/doc/autodock/ --- From chemistry-request@ccl.net Fri Jul 9 16:39:41 2004 Received: from rwcrmhc12.comcast.net (rwcrmhc12.comcast.net [216.148.227.85]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69Ldcga014559 for >ccl.net>; Fri, 9 Jul 2004 16:39:38 -0500 Received: from planaria (c-24-18-160-79.client.comcast.net[24.18.160.79]) by comcast.net (rwcrmhc12) with SMTP id <2004070921452701400li50ue>; Fri, 9 Jul 2004 21:45:27 +0000 Reply-To: >arguslab.com> From: "Mark Thompson" >arguslab.com> To: "Pandey, Jaya" >chla.usc.edu>, >ccl.net> Subject: RE: Docking tool Date: Fri, 9 Jul 2004 14:45:17 -0700 Message-ID: <000401c465fe$0685b120$0200a8c0@planaria> 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 9.0.6604 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 Importance: Normal In-Reply-To: <73564B8DE398D61180500008C75D7E49033E5FE4@NTMAIL03> X-Spam-Status: No, hits=3.7 required=7.5 tests=FVGT_m_MULTI_ODD2, RCVD_IN_DYNABLOCK,RCVD_IN_SORBS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Soon....ArgusLab 4.0 I'm preparing results for a poster at the ACS and will release the code shortly thereafter. It supports both interactive docking and database screens (sdf file format for the ligand database). Here are some typical timings for interactive dockings on a 2.4 GHz pentium laptop. Target Ligand Torsions Time (sec) -------------------------------------------------- 1HPV VX478 14 21 1ADB CNAD 11 14 1HVR XK263 8 16 4DFR Methotrexate 9 3 1IEP Gleevec 7 11 1CBX Benzylsuccinate 5 5 1STP Biotin 5 3 3PTB Benzamidine 0 1 Mark *************************** Mark Thompson Planaria PO Box 55207 Seattle, WA 98155 mark<>arguslab.com http://www.arguslab.com *************************** -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request<>ccl.net]On Behalf Of Pandey, Jaya Sent: Friday, July 09, 2004 12:00 PM To: 'chemistry<>ccl.net' Subject: CCL:Docking tool Dear All, Does anyone know of a efficient docking freeware that can be used for a rapid drug screening library. I am using AutoDock currently but unfortunately I am not very comfortable with it for a rapid screen. Any clues?? Thanks Jaya -= This is automatically added to each message by the mailing script =- To send e-mail to subscribers of CCL put the string CCL: on your Subject: line and send your message to: CHEMISTRY<>ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST<>ccl.net HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs If your mail is bouncing from CCL.NET domain send it to the maintainer: Jan Labanowski, jlabanow<>nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Fri Jul 9 15:03:33 2004 Received: from mx5.net.nih.gov (mx5.net.nih.gov [165.112.130.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69K3WUW012691 for ; Fri, 9 Jul 2004 15:03:32 -0500 Received: from mx5.net.nih.gov (localhost [127.0.0.1]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i69K9NMK000752 for ; Fri, 9 Jul 2004 16:09:23 -0400 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by mx5.net.nih.gov (8.12.10/8.12.8p1) with ESMTP id i69K9N61000711; Fri, 9 Jul 2004 16:09:23 -0400 Date: Fri, 9 Jul 2004 16:06:48 -0400 From: Rick Venable To: h9807907=at=hkusua.hku.hk cc: CHEMISTRY=at=ccl.net Subject: Re: CCL:Questions about CHARMM I/O In-Reply-To: <1089366908.40ee6b7c24f87=at=imp.webmail.hku.hk> Message-ID: References: <1089366908.40ee6b7c24f87=at=imp.webmail.hku.hk> ReplyTo: Rick_Venable=at=nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=1.5 required=7.5 tests=MAILTO_TO_SPAM_ADDR autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Reminder: try the CHARMM Forums at www.charmm.org for questions about using academic CHARMM. (Questions about using the commercial CHARMm product via Quanta or InSight should be directed to Accelrys). On Fri, 9 Jul 2004 h9807907=at=hkusua.hku.hk wrote: > I am new to CHARMM and I hope that you can give me some ideas of the following > questions. > 1) Do anyone know how to print out the coordinate file and restart file at > different time intervals during a MD similation? Is that possible by modifying > the .inp file? The coordinates are saved in the trajectory file indicated by IUNCRD every NSAVC integration steps; change NSAVC to change the frequency for saving coordinate sets. By default, the restart file is only written once, at the end of the run; for modern computer systems with low failure rates, this is the preferred method. The ISVFRQ option of DYNAmics can be used to write the restart file (to the unit specified by IUNWRI) more often. > 2) How can I suppress the print of those files, such as .vel .ene, which I > cannot read? Don't open the files and assign unit numbers, and don't specify a frequency (in integration steps) for these, i.e. the DYNAmics command would include IUNVEL -1 NSAVV 0 KUNIT -1 The .ene file should be readable, just not easily understood. =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= 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 =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= From chemistry-request@ccl.net Fri Jul 9 17:53:06 2004 Received: from acomp.usf.edu (acomp.usf.edu [131.247.100.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i69Mr4ga015709 for ; Fri, 9 Jul 2004 17:53:04 -0500 Received: from [131.247.209.78] (HELO WILL) by acomp.usf.edu (CommuniGate Pro SMTP 4.1.5) with ESMTP id 7709809 for chemistry(at)ccl.net; Fri, 09 Jul 2004 18:58:56 -0400 From: "will" To: Subject: get-dockings command in autodock problems Date: Fri, 9 Jul 2004 18:58:44 -0400 Message-ID: <000001c46608$4c16f140$4ed1f783@WILL> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0001_01C465E6.C5055140" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2616 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1409 X-Spam-Status: No, hits=0.1 required=7.5 tests=HTML_70_80,HTML_MESSAGE autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net This is a multi-part message in MIME format. ------=_NextPart_000_0001_01C465E6.C5055140 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Upon giving this command, I get the following error: Sed: can't open fixatomnames.sed (can't find file or directory) The file is in the same folder that the 'get-dockings' command is in, so I'm not sure how it can 'not find' the file. Also, the prepare command mentioned in the autodock manual doesn't seem to exist in my distribution. Prepare-gpf+dpf works fine, but 'prepare m s' where m is macro and s substrate doesn't seem to be on my computer. Job3 gives the error: Autodock_uti: undefined variable While job gives: Autodock_root: undefined variable Unfortunately, I have no real experience with linux and am not sure how to fix these problems. I tried the "setenv. " and "set path=$path $autodock_uti" as mentioned in the manual, but I don't even know if that has anything to do with the problems I'm experiencing now. I'm running cygwin on windows xp in case that's pertinent. Thanks for the help in advance. Will University of South Florida Department of Chemistry and Biochemistry ------=_NextPart_000_0001_01C465E6.C5055140 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Upon giving this command, I get the following = error:

 

Sed: can’t open fixatomnames.sed  = (can’t find file or directory)

 

The file is in the same folder that the = ‘get-dockings’ command is in, so I’m not sure how it can ‘not find’ = the file.  Also, the prepare = command mentioned in the autodock manual = doesn’t seem to exist in my distribution.  = Prepare-gpf+dpf works fine, but ‘prepare m s’ = where m is macro and s substrate doesn’t seem to be on my computer.  Job3 gives the = error:

 

Autodock_uti:  undefined = variable

 

While job gives:

 

Autodock_root<= /span>:  undefined = variable

 

Unfortunately, I have no real experience with linux and am not sure how to fix these = problems.  I tried the “setenv… “ and “set path=3D$path $autodock_uti” as mentioned in the manual, but I don’t even know if that has = anything to do with the problems I’m experiencing now.  I’m running cygwin on windows xp in case that’s = pertinent.  Thanks for the help in = advance.

 

Will

University of = South = Florida

Department of Chemistry and = Biochemistry

------=_NextPart_000_0001_01C465E6.C5055140--