From chemistry-request@ccl.net Mon Jan 19 09:45:54 2004 Received: from maui.ebi.ac.uk (maui.ebi.ac.uk [193.62.196.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0JEjqc1026541 for ; Mon, 19 Jan 2004 09:45:53 -0500 Received: from ebi.ac.uk (vlamingh.ebi.ac.uk [172.22.8.120]) by maui.ebi.ac.uk (8.11.7+Sun/8.11.7) with ESMTP id i0JEkfm05867 for ; Mon, 19 Jan 2004 14:46:49 GMT Message-ID: <400BEDC7.4050501=at=ebi.ac.uk> Date: Mon, 19 Jan 2004 14:46:31 +0000 From: Janet Copeland User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031007 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY=at=ccl.net Subject: EMBO course - 3D structure databases - uses for biological problem solving Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-EBI-Information: This email is scanned using www.mailscanner.info. X-EBI: Found to be clean X-EBI-SpamCheck: not spam, SpamAssassin (score=-5.8, required 5, USER_AGENT_MOZILLA_UA -5.80) X-Spam-Status: No, hits=0.0 required=7.0 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 EMBO Workshop 19 - 24 September 2004 Registration for this workshop is now open. Please see http://www.ebi.ac.uk/msd/news-events/EMBO.html for details of the course and access to on-line registration page The course will teach the basic principles; aspects of 3D database technology and the associated tools for data analysis to bioscientists wishing to understand the wealth of structure information available. The course is primarily aimed at PhD students and postdocs to give them a familiarity with how structure data can be used in their own projects. Databases for 3D structural data for proteins and nucleic acids, together with the associated access tools have matured into a major tool for molecular biology. The course is intended to cover the background to relational databases and the computational aspects of characterizing structure of biological macromolecules. Co-organizers Professor Janet Thornton (European Bioinformatics Institute) Dr Gerard Kleywegt (Uppsala University) Dr Jaime Prilusky (Weizmann Institute of Science) Dr Helen Berman (Rutgers, the State University of New Jersey) Janet Copeland Workshop co-ordinator ~~~~~~~~~~~~~~~~ From chemistry-request@ccl.net Mon Jan 19 06:19:55 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 i0JBJsc1018176 for ; Mon, 19 Jan 2004 06:19:54 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AiXSe-000NGRC; Mon, 19 Jan 2004 12:20 +0100 Message-ID: <400BBE3E.4030102(at)chem.vu.nl> Date: Mon, 19 Jan 2004 12:23:42 +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: CCL posting Subject: Re: CCL:Multiple Simulations References: <4002C121.10206(at)chem.vu.nl> <23909.1074064380(at)www61.gmx.net> In-Reply-To: <23909.1074064380(at)www61.gmx.net> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 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 Bimo Ario Tejo wrote: > Dear Dr. Anton, > > Have you received any respond from the list regarding your question? I have > the same question with yours but until now I still have no idea how to solve > it. Not from the CCL, but I posted the same question on the Gromacs users list, and got this answer from David L. Bostick: Yes, there is a way to combine statistics from various simulations of the same system. Assuming, of course, that all systems are in equilibrium. Assuming equilibrium, of course, allows us to avoid the problems mentioned by Anton (homology models vs. x-ray structures ..etc.). If the conditions (i.e. N,P, and T) are the same the average is linear. However there are recently (~1990s) developed methods for overcoming barriers for rare events in simulations by holding many simultaneous simulations at different temperatures. It was first designed for Monte Carlo of glassy systems. The data from these simulations can be combined via multiple histogram methods. The method is called Parallel Tempering and has been recently implemented in MD simulation under the name of "Replica Exchange Molecular Dynamics." A good description of the background can be found in: Monte Carlo Methods in Statistical Physics by M.E.J. Newman and G.T. Barkema (1999) Clarendon Press, Oxford. And for the MD implementation, Sugita, Y. and Okamoto, Y. Replica-exchange Molecular Dynamics Method for Protein Folding. Chemical Physics Letters 314 (1999) 141-151. -- 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 Mon Jan 19 03:05:32 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 i0J85Vc1013178 for ; Mon, 19 Jan 2004 03:05:31 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AiUQR-000NGMC; Mon, 19 Jan 2004 09:06 +0100 Message-ID: <400B821E.4040603(at)chem.vu.nl> Date: Mon, 19 Jan 2004 08:07:10 +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: reynier(at)fq.uh.cu CC: chemistry(at)ccl.net Subject: Re: CCL:Software to build topology files for Gromos automatically? References: <01c601c3dbb9$6f90d020$2c03a8c0(at)qct.fq.oc.uh.cu> In-Reply-To: <01c601c3dbb9$6f90d020$2c03a8c0(at)qct.fq.oc.uh.cu> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 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 reynier(at)fq.uh.cu wrote: > Hi > I'm trying to use Gromos to performed a MD of some small molecules. > Does anybody knows about a software to automaticaly build the topology > files for moleculos non known by Gromos? ProDrg can do that. There is a web-server somewhere where you can enter your molecule (as a .pdb file or schematic drawing). Typing 'prodrg' in google should find it for you... -- 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 Mon Jan 19 03:05:25 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 i0J85Oc1013152 for ; Mon, 19 Jan 2004 03:05:25 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AiUQQ-000NGIC; Mon, 19 Jan 2004 09:06 +0100 Message-ID: <400B8020.4060108(at)chem.vu.nl> Date: Mon, 19 Jan 2004 07:58:40 +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: Bimo Ario Tejo CC: chemistry(at)ccl.net Subject: Re: CCL:residue cross correlation References: <27031.1074268337(at)www53.gmx.net> In-Reply-To: <27031.1074268337(at)www53.gmx.net> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.0 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 Bimo Ario Tejo wrote: > Dear all, > > I'm just wondering does anyone have a program to calculate residue > cross-correlation (DCCM) of MD trajectories based on vectors (origin at mean atom > position during simulation)? I need such a program that able to read any > trajectories regardless what program used (CHARMM, Amber, Gromacs, etc.)... AFAIK, there is no common trajectory format, not even one that is recognized by more than a few programs... ;-{ What I do know, is that most programs can write pdb files, and also most can read them again. Gromacs can recognize concatenated pdb files as a trajectory, and can read and write it as a native format (although slower than most other formats, and huge amounts of diskspace...) I'm not sure which correlations you mean, but I'm pretty sure it is possible to calculate them with one of the many analysis tools of Gromacs. -- 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 Mon Jan 19 09:57:56 2004 Received: from jp-ns-1.it.actelion.com ([219.166.110.58]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0JEvsc1027052 for ; Mon, 19 Jan 2004 09:57:55 -0500 Received: from jp-ns-1.it.actelion.com (localhost.localdomain [127.0.0.1]) by localhost.it.actelion.com (MailSystem) with ESMTP id 944C11AA5B6 for ; Mon, 19 Jan 2004 15:58:45 +0100 (CET) Received: from ActelChMail.Actelion.Com (actelch13.europe.actelion.com [10.100.0.21]) by jp-ns-1.it.actelion.com (MailSystem) with ESMTP id 0E30C1AA570 for ; Mon, 19 Jan 2004 15:58:45 +0100 (CET) Subject: MM2 ForceField in Java To: chemistry*at*ccl.net Message-ID: From: Joel.Freyss*at*Actelion.Com Date: Mon, 19 Jan 2004 15:58:42 +0100 MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii X-Spam-Checked-By: jp-ns-1.it.actelion.com X-Spam-Status: No, hits=0.3 required=7.0 tests=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 Hello, I am trying to implement a MM2 forcefield in Java. I found Tinker to be a great help for that work but I wondered if anybody ever tried to develop something like that in Java and has some hints or resources to help me? I need to find a position close to a global minimum in a very short amount of time and the forcefield needs to be reliable. Right now, I implemented the bond stretching, angle bending, torsion and VDW parameters and I get approximative results in about 2s: CH bonds with a length of 1.05 A, using the simulated annealing and then the steepest descent algorithm. Any advise? Thanks Joel ************************************************************************* The information of this e-mail and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this e-mail is prohibited and may be unlawful. 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For further information about Actelion please see our website at http://www.actelion.com. ************************************************************************** From chemistry-request@ccl.net Mon Jan 19 12:23:53 2004 Received: from postoffice7.mail.cornell.edu (postoffice7.mail.cornell.edu [132.236.56.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0JHNqc1000492 for ; Mon, 19 Jan 2004 12:23:52 -0500 Received: from cornell.edu (cs6711168-41.satx.rr.com [67.11.168.41]) by postoffice7.mail.cornell.edu (8.12.10/8.12.6) with ESMTP id i0JHOYgk020643; Mon, 19 Jan 2004 12:24:51 -0500 (EST) Message-ID: <400C12D1.70408*at*cornell.edu> Date: Mon, 19 Jan 2004 11:24:33 -0600 From: Richard Wood User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.4) Gecko/20030624 Netscape/7.1 (ax) X-Accept-Language: en-us, en MIME-Version: 1.0 To: "chemistry*at*ccl.net" Subject: Re: CCL:residue cross correlation References: <27031.1074268337*at*www53.gmx.net> <400B8020.4060108*at*chem.vu.nl> In-Reply-To: <400B8020.4060108*at*chem.vu.nl> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hi all If one used CHARMm/CHARMM to calculate these trajectories, why can't one use CHARMm/CHARMM to analyse them? Richard Anton Feenstra wrote: > Bimo Ario Tejo wrote: > >> Dear all, >> >> I'm just wondering does anyone have a program to calculate residue >> cross-correlation (DCCM) of MD trajectories based on vectors (origin >> at mean atom >> position during simulation)? I need such a program that able to read any >> trajectories regardless what program used (CHARMM, Amber, Gromacs, >> etc.)... > > > AFAIK, there is no common trajectory format, not even one that is > recognized > by more than a few programs... ;-{ > What I do know, is that most programs can write pdb files, and also most > can read them again. Gromacs can recognize concatenated pdb files as a > trajectory, and can read and write it as a native format (although slower > than most other formats, and huge amounts of diskspace...) I'm not sure > which correlations you mean, but I'm pretty sure it is possible to > calculate > them with one of the many analysis tools of Gromacs. > > From chemistry-request@ccl.net Mon Jan 19 14:39:04 2004 Received: from antivirus1.its.rochester.edu (antivirus1.its.rochester.edu [128.151.57.50]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0JJd4c1004705 for ; Mon, 19 Jan 2004 14:39:04 -0500 Received: from antivirus1.its.rochester.edu (localhost [127.0.0.1]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with ESMTP id i0JJe2XD022445 for ; Mon, 19 Jan 2004 14:40:02 -0500 (EST) Received: from mail.rochester.edu (mail1.ats.rochester.edu [128.151.224.31]) by antivirus1.its.rochester.edu (8.12.9/8.12.4) with SMTP id i0JJdx71022425 for ; Mon, 19 Jan 2004 14:40:01 -0500 (EST) Received: from mail.rochester.edu (mail.rochester.edu [128.151.224.17]) by mail.rochester.edu (8.12.10/8.12.1) with SMTP id i0JJdsnJ025266 for ; Mon, 19 Jan 2004 14:39:58 -0500 (EST) Sender: weiz.-at-.mail.rochester.edu From: "weiz" Reply-to: weiz.-at-.mail.rochester.edu To: chemistry.-at-.ccl.net Subject: help about gaussian X-Mailer: Quality Web Email v3.0q, http://netwinsite.com/refw.htm Date: Mon, 19 Jan 2004 14:39:54 -0500 Priority: normal Message-id: <400c328a.62b0.7507.-at-.mail.rochester.edu> Hi,All: if I want to do a Geometry optimization of two 10-atom small molecules surrounded by 120 partial charges, is the computing feasible for a single AMD 240 processor? I am using B3LYP/6-31G level. another question is: how much longer is the computing time compared with the Geometry optimization of the same two molecules without the partial charges? All the Best Wei Zhuang From chemistry-request@ccl.net Mon Jan 19 12:18:48 2004 Received: from mtiwmhc12.worldnet.att.net (mtiwmhc12.worldnet.att.net [204.127.131.116]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0JHIjc1000336 for ; Mon, 19 Jan 2004 12:18:46 -0500 Received: from zinc.fujitsu.com (91.denver-06rh15rt.co.dial-access.att.net[12.73.181.91]) by worldnet.att.net (mtiwmhc12) with SMTP id <2004011917193511200pq8jqe>; Mon, 19 Jan 2004 17:19:35 +0000 Message-Id: <6.0.1.1.2.20040119101059.02795040|at|postoffice.worldnet.att.net> X-Sender: mrmopac|at|postoffice.worldnet.att.net X-Mailer: QUALCOMM Windows Eudora Version 6.0.1.1 Date: Mon, 19 Jan 2004 10:17:20 -0700 To: chemistry|at|ccl.net From: "James J. P. Stewart" Subject: CCL: Slater orbital p - d transition probabilities Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii"; format=flowed Help! I'm trying to derive the oscillator integral, os, for p to d transitions in an atom, and have come up with the expression: os = (np+nd+1)!*2**(np+nd+1)*exp(p)**(np+1/2)*exp(d)**(nd+1/2) -------------------------------------------------------- sqrt(5)*(exp(p)+exp(d)**(np+nd+2)*sqrt( (2*np)! * (2*nd)! ) where the Slater orbital principal quantum numbers are "np" and "nd", and the exponents are "p" and "d". Can anyone confirm or dispute this expression, please. Evidence either way would be appreciated. My concern is that the integral becomes very large for large values of "np" and "nd". Thanks, Jimmy From chemistry-request@ccl.net Mon Jan 19 12:12:52 2004 Received: from ncsusraimge01.jnj.com (ncsusraimge01.jnj.com [148.177.2.21]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id i0JHCkc1032598 for ; Mon, 19 Jan 2004 12:12:51 -0500 Received: from NCSUSRAWSC2.na.jnj.com (NCSUSRAWSC2.na.jnj.com [10.4.20.22]) by ncsusraimge01.jnj.com (Switch-3.1.2/Switch-3.1.0) with SMTP id i0JHDWNT016857 for ; Mon, 19 Jan 2004 12:13:40 -0500 (EST) Received: From ncsusraexims2.rar.ncsus.jnj.com ([150.13.1.40]) by NCSUSRAWSC2.na.jnj.com (WebShield SMTP v4.5 MR1a); id 107453241015; Mon, 19 Jan 2004 12:13:30 -0500 Received: by ncsusraexims2.rar.ncsus.jnj.com with Internet Mail Service (5.5.2657.72) id ; Mon, 19 Jan 2004 12:13:20 -0500 Message-ID: <052DFACABA03D7119E9E0002A544D167033E94B5{at}prdusraexs23.ncs.jnj.com> From: "Cummings, Maxwell D. [3DP]" To: "'chemistry{at}ccl.net'" Cc: "'martin{at}yangtze.hku.hk'" Subject: RE: How to define a dummy atom in Charmm (and InsightII) Date: Mon, 19 Jan 2004 12:05:16 -0500 MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.5.2657.72) Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3DEAE.1F8B53AA" This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C3DEAE.1F8B53AA Content-Type: text/plain In insight this is the Pseudo_Atom pulldown in the Builder module. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request{at}ccl.net]On Behalf Of martin{at}yangtze.hku.hk Sent: Saturday, January 17, 2004 5:05 AM To: chemistry{at}ccl.net Subject: CCL:How to define a dummy atom in Charmm Dear sirs, I am sorry to post questions again and again. I would like to ask how to define a dummy atom in Charmm or insightII. Thank you very much Martin -= 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{at}ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST{at}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{at}nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ ------_=_NextPart_001_01C3DEAE.1F8B53AA Content-Type: text/html Content-Transfer-Encoding: quoted-printable RE: How to define a dummy atom in Charmm (and InsightII)

In insight this is the Pseudo_Atom pulldown
in the Builder module.

-----Original Message-----
From: Computational Chemistry List [mailto:chemistry-request@ccl.n= et]On
Behalf Of martin{at}yangtze.hku.hk
Sent: Saturday, January 17, 2004 5:05 AM
To: chemistry{at}ccl.net
Subject: CCL:How to define a dummy atom in = Charmm


Dear sirs,

I am sorry to post questions again and again. I would = like to ask how to
define a dummy atom in Charmm or insightII.

Thank you very much

Martin



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