From chemistry-request@server.ccl.net Tue Feb 6 01:46:40 2001 Received: from vytautas.vdu.lt (mail@vytautas.vdu.lt [193.219.38.33]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f166fVw23372 for ; Tue, 6 Feb 2001 01:41:58 -0500 Received: from vaidila.vdu.lt ([193.219.38.52] ident=root) by vytautas.vdu.lt with esmtp id 14Q1oF-0000et-00; Tue, 06 Feb 2001 08:41:03 +0200 Received: from vaidila.vdu.lt (vejas.vdu.lt [193.219.38.82]) by vaidila.vdu.lt (8.9.3/8.9.3) with ESMTP id IAA15658; Tue, 6 Feb 2001 08:41:03 +0200 (GMT) Message-ID: <3A7F0150.98C33A28@vaidila.vdu.lt> Date: Mon, 05 Feb 2001 20:38:57 +0100 From: "art'" X-Mailer: Mozilla 4.7 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: Qin Wu CC: chemistry@ccl.net Subject: Re: CCL:Error messages from Gaussian References: <200102052207.RAA0000000604@carrot.chem.duke.edu> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Hi, Qin, It would be better you to explain what kind of job you run ... Arturas Z. Qin Wu wrote: > Dear all, > Does anybody know a place that has the explanations for the error messages in running > Gaussian? Personally I met a message as follows: > "Erroneous read. Read -1 instead of 200. > fd = 3" > It's hard for me to tell what's wrong. Some explanations will be very useful, I think. > Thanks in advance. > Qin > > -= 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 Tue Feb 6 12:03:43 2001 Received: from simak.acpub.duke.edu (simak.acpub.duke.edu [152.3.232.12]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16H3hw25717 for ; Tue, 6 Feb 2001 12:03:43 -0500 Received: from godzilla1.acpub.duke.edu (zl2@godzilla1.acpub.duke.edu [152.3.233.42]) by simak.acpub.duke.edu (8.9.3/8.9.3/Duke-5.0.0) with SMTP id MAA26589; Tue, 6 Feb 2001 12:03:44 -0500 (EST) Date: Tue, 6 Feb 2001 12:03:36 -0500 (EST) From: Zhenyu Lu X-Sender: zl2@godzilla1.acpub.duke.edu To: chemistry@ccl.net Subject: Help on Gaussian Error Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All: I am using Gaussian 98 to do some optimization, but it stops after several optimization steps and give out the following error message: 1 Symmetry operations used in ECPInt. ECPInt: NShTT= 10585 NPrTT= 42446 LenC2= 7399 LenP2D= 18527. LDataN: DoStor=F MaxTD1= 6 Len= 172 LDataN: DoStor=T MaxTD1= 6 Len= 172 ECPSu allocation failure: iend,mxcore= 1345271 1345270 Error termination via Lnk1e .... I am using pseudo-potentials for some elements. My question is: what's the error mean? why does the calculation seem working well in previous steps but suddenly get crashed? Thanks in Advance! Zhenyu From chemistry-request@server.ccl.net Tue Feb 6 12:08:50 2001 Received: from mail.chem.tamu.edu (mail.chem.tamu.edu [165.91.176.8]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16H8ow25768 for ; Tue, 6 Feb 2001 12:08:50 -0500 Received: from mail.chem.tamu.edu ([165.91.177.32]) by mail.chem.tamu.edu (Post.Office MTA v3.5.3 release 223 ID# 0-64333U1000L100S0V35) with ESMTP id edu for ; Tue, 6 Feb 2001 11:20:13 -0600 Sender: yubo@ccl.net Message-ID: <3A7FDB85.A115722D@mail.chem.tamu.edu> Date: Tue, 06 Feb 2001 11:09:57 +0000 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: DFT for hydrogen bond Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone, I know most of DFT methods are not good to the calculation of Hydrogen Bonding. But a friend of mine told me somebody developed a DFT method that can be used in HB calculations. What is this method? Are there some papers using different methods (DFT methods preferred) to calculate HB and systematically compare them? Any advice is helpful. Thanks in Advance Yubo Fan -- ============================================================ Dr. Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Tue Feb 6 01:13:52 2001 Received: from mail.etang.com (mail.etang.com [202.101.42.207] (may be forged)) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f166Dnw23298 for ; Tue, 6 Feb 2001 01:13:50 -0500 Received: from ns (unknown [202.109.98.131]) by mail.etang.com (Postfix) with SMTP id 624021CA5F5E1 for ; Tue, 6 Feb 2001 14:21:01 +0800 (CST) Message-ID: <001401c09004$0d54bce0$cd0b140a@fudan.edu.cn> From: "jewar" To: Subject: high symmetry k-points Date: Tue, 6 Feb 2001 14:14:24 +0800 Dear all, I want to investigate the band structures of some transitional metals surfaces. There are some question: How to chose the special k-points for the different surfaces such as (111), (100) and (110) surface? Where to find the the coordinate of some high symmetry k-points such as M, S points? With best regards! Yun Wang Chemical Department Fudan University Shanghai, China From chemistry-request@server.ccl.net Tue Feb 6 02:35:18 2001 Received: from elin.scali.no (elin.scali.no [195.139.250.10]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f167ZHw23525 for ; Tue, 6 Feb 2001 02:35:17 -0500 Received: from scali.no (IDENT:ole@pc-4.scali.no [172.16.0.104]) by elin.scali.no (8.9.3/8.8.7) with ESMTP id IAA07322 for ; Tue, 6 Feb 2001 08:35:17 +0100 Sender: ole@scali.no Message-ID: <3A7FA92E.9254142B@scali.no> Date: Tue, 06 Feb 2001 08:35:10 +0100 From: "Ole W. Saastad" X-Mailer: Mozilla 4.72 [en] (X11; U; Linux 2.2.14-5.0 i686) X-Accept-Language: no, en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Parallel Gaussian Performance Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Parallel Gaussian Gaussian Inc. supplies a parallel version of g98 that uses Linda from Scientific Computing Associates. My questions are concerned about how well does the combination of g98 and Linda perform? How well does it scale ? Do memory requirements also scale well ? What are the experience of the cluster users around ? I am interested in performance of Linda and Gaussian on linux clusters, both standard Beowulf clusters and tightly coupled clusters with Myrinet or Dolphin interconnect. How is the communication done with Linda ? The paradigm is "tuple space", but in reality some underlying layer must be present. How is this done ? Shared memory model or message passing ? I have seen (posted somewhere on the net) that there exist a MPI version of g94/g98. Have anyone experience with this version of g98(g94) ? A MPI version of Gaussian would not require the purchase of the Linda system. For clusters with fast interconnect and fast MPI the MPI version of g98 is expected to yield higher performance than Linda/g98. How is this in practice ? Have anyone experience of running the MPI Gaussian on a cluster of Linux machines ? Again how is the performance on Beowulf, Myrinet or Dolphin interconnected systems ? How well does it scale ? When does it start to roll off (at 16 cpus or 32, 64 or even higher?). Best regards Ole W Saastad From chemistry-request@server.ccl.net Tue Feb 6 07:08:55 2001 Received: from coch11.chm.tu-dresden.de (mann@coch11.chm.tu-dresden.de [141.30.9.111]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16C8tw24926 for ; Tue, 6 Feb 2001 07:08:55 -0500 Received: from localhost (localhost [[UNIX: localhost]]) by coch11.chm.tu-dresden.de (8.9.3/8.9.3) id NAA26809; Tue, 6 Feb 2001 13:08:43 +0100 From: Matthias Mann Reply-To: Matthias.Mann@chemie.tu-dresden.de To: CHEMISTRY@ccl.net Subject: Linux 2.4.0 and 2 GB promlem Date: Tue, 6 Feb 2001 12:45:35 +0100 X-Mailer: KMail [version 1.0.17] Content-Type: text/plain Cc: q_timerg@alcor.concordia.ca MIME-Version: 1.0 Message-Id: <01020613084300.26802@coch11> Content-Transfer-Encoding: 8bit X-KMail-Mark: Hallo, > Dear CCL'ers, > I've heard that new Linux kernel 2.4.0 can handle files larger than 2 GB. > Have anybody tried to test 2.4.0 kernel with quantum-chemical programs? it seems, nobody has experience with this until now ? Because I'm also very interested to solve this problem, I asked Gaussian according the LFS support in G98. Here is the answer: > The limit is partly relieved in Rev. A.7. We have further > changes expected in the next minor revision which should > remove it entirely for machines with native 64 bit integers. > For A.7 the limit is around 20GB due to a limit in the bin > sort required for post-MP2 methods. > > This does not extend to Linux on Intel platforms because here > 32 bit integers are still used to maintain good performance. > We have not yet tested with the 2.4 kernels but since we see > as bad as 30% penalty for using 64 bit integers on machines > like the IBM Power3 when using 64 bit integers we don't plan on > releasing a version for Linux on Intel. This is not totally clear, because it is possible to support large files also on 32 bit systems. For example, large files are supported with 32bit IBM AIX 4.2 on RS/6000 (without reducing performance). Because the 2 GB limit is one of the remaining disadvantages in comparison of Linux systems with commercial workstations, we should try to solve this for quantum chemical programs ?! Greetings, Matthias -- Dr. Matthias Mann Institut fuer Organische Chemie, TU Dresden D-01069 Dresden, Mommsenstr. 13 Tel.: +49 (351) 463-4286 / Fax: -3162 Email: Matthias.Mann@chemie.tu-dresden.de From chemistry-request@server.ccl.net Tue Feb 6 11:29:11 2001 Received: from mailrouter1.strath.ac.uk (orkney.cc.strath.ac.uk [130.159.248.40]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16GTBw25628 for ; Tue, 6 Feb 2001 11:29:11 -0500 Received: from pc143-ren16.cable.ntl.com ([62.253.183.143] helo=strath.ac.uk) by mailrouter1.strath.ac.uk with esmtp (Exim 3.12 #2) id 14QAz3-0005QM-00; Tue, 06 Feb 2001 16:28:49 +0000 Message-ID: <3A80266D.70D7C598@strath.ac.uk> Date: Tue, 06 Feb 2001 16:29:33 +0000 From: "Dr. Peter Bladon" To: CHEMISTRY@ccl.net Subject: What is a structural representation in chemistry? Dear colleagues, This is a very interesting paper, but perhaps not for the reasons intended by the authors. In particular, in the second paragraph of section 7 (just before the references) the authors say "We are currently developing the software as well as preparing the patent related to the application of the proposed model to CADD". Are we to expect that if the proposed framework is adopted widely (as I presume the authors hope) others will be prevented from making use of the information in the paper without paying royalties? After all, the original email from Dr Goldfarb would count as disclosure prior to the granting of a patent. In any case is this the correct way to go about things? Yours sincerely Peter Bladon From chemistry-request@server.ccl.net Tue Feb 6 13:31:31 2001 Received: from Post-Office.UH.EDU (Post-Office.UH.EDU [129.7.1.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16IVVw26312 for ; Tue, 6 Feb 2001 13:31:31 -0500 Received: from CONVERSION-DAEMON by Post-Office.UH.EDU (PMDF V5.2-32 #40812) id <0G8C00E01M4GU6@Post-Office.UH.EDU> for CHEMISTRY@ccl.net; Tue, 6 Feb 2001 12:31:28 -0600 (CST) Received: from uh.edu (Kroll.BCHS.UH.EDU [129.7.2.217]) by Post-Office.UH.EDU (PMDF V5.2-32 #40812) with ESMTP id <0G8C00E43M4GHF@Post-Office.UH.EDU> for CHEMISTRY@ccl.net; Tue, 06 Feb 2001 12:31:28 -0600 (CST) Date: Tue, 06 Feb 2001 12:29:39 -0600 From: Hung-Chung Huang Subject: Two questions about MD and NAMD2.2! To: CHEMISTRY@ccl.net Message-id: <3A804293.8080805@uh.edu> MIME-version: 1.0 Content-type: text/plain; charset=us-ascii; format=flowed Content-transfer-encoding: 7bit User-Agent: Mozilla/5.0 (Windows; U; WinNT4.0; en-US; m18) Gecko/20001108 Netscape6/6.0 X-Accept-Language: en,pdf Dear CCLers, I have two questions about running MD simulations with NAMD 2.2 from UI (http://www.ks.uiuc.edu). 1. After I finished 60ps equilibration by using temperature reassignment method (from 50K to 300K gradually) of NAMD2.2, the system looked very stable around 300K (especially in the last 20ps of equilibration). But why the system's temperature kept increasing after I went to the MD phase simulations? P.S., I used temperature coupling , Berendsen pressure bath coupling, and no PME. 2. When I tried PME and if I positioned the ions (e.g. sodium ions) on the edge of water box, the ions would leave the box and cause problems. Is there any way to confine the sodium ions in the box (e,g., with "wrapWater" on, waters can be wrapped back to another side of box if they move out of the box)? Or what's the criterion to position ions close to the protein for PME? Your hints or suggestions will be much appreciated!!! Joe -- http://adrik.bchs.uh.edu/~jhuang From chemistry-request@server.ccl.net Tue Feb 6 13:53:46 2001 Received: from postoffice.mail.cornell.edu (postoffice.mail.cornell.edu [132.236.56.7]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16Irkw26357 for ; Tue, 6 Feb 2001 13:53:46 -0500 Received: from cornell.edu (carbo2.foodsci.cornell.edu [132.236.147.61]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id NAA06189 for ; Tue, 6 Feb 2001 13:53:46 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3A8046B4.ED67389F@cornell.edu> Date: Tue, 06 Feb 2001 13:47:16 -0500 From: "Dr. Richard Wood" Organization: Cornell University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Some more CHARMM questions Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I've got a nanosecond dynamics trajectory of a solvated protein. I wish to calculate the following form the trajectory (actually, the trajectory is in several pieces, but that doesn't matter): The psi's and phi's as a function of time, the number of hydrogen bonds, and the number of shared waters. I've been through the CHARMM "manual", but I haven't found any insight in how to do this. Any one have any suggestions? Thanks, Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Tue Feb 6 15:25:30 2001 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16KPTw26749 for ; Tue, 6 Feb 2001 15:25:29 -0500 Received: from geneseo.ks.uiuc.edu (geneseo.ks.uiuc.edu [130.126.120.127]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id OAA10156 for ; Tue, 6 Feb 2001 14:25:30 -0600 (CST) Received: (from johns@localhost) by geneseo.ks.uiuc.edu (8.9.3+Sun/8.9.1) id OAA01710 for chemistry@ccl.net; Tue, 6 Feb 2001 14:25:30 -0600 (CST) Date: Tue, 6 Feb 2001 14:25:30 -0600 From: John Stone To: chemistry@ccl.net Subject: Announce: Struc. Bio. Software Database Message-ID: <20010206142529.L994@geneseo.ks.uiuc.edu> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 1.0i Structural Biology Software Database Announcement ------------------------------------------------- The Theoretical Biophysics group at the Beckman Institute at the University of Illinois, is proud to announce the public release of the initial version of a "Structural Biology Software Database". We have created a web-based database containing programs which are thought to be of interest to researchers in the fields of structural biology, quantum chemistry, and bioinformatics. The database is still young, and we are continuosly working on improving its interface and content, but it is ready for the community to use. We encourage users to send the developers and moderators suggestions for improvements, and new application submissions for the database itself. The source code for the database is now available, so that others can create their own software databases to serve application domains not included in our database. We welcome any ideas or feedback that you would like to share with us. The database is located within the "MDSalon" at: http://www.ks.uiuc.edu/Services/MDSalon or directly via: http://www.ks.uiuc.edu/Development/biosoftdb The "SoftDB" source code (which implements the DB) is available from: http://www.ks.uiuc.edu/Development/MDTools/softdb/ Thanks!! John Stone biosoftdb@ks.uiuc.edu February 6, 2001 -- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns@ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078 From chemistry-request@server.ccl.net Tue Feb 6 16:26:24 2001 Received: from havana.ks.uiuc.edu (havana.ks.uiuc.edu [130.126.120.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16LQOw27089 for ; Tue, 6 Feb 2001 16:26:24 -0500 Received: from verdun.ks.uiuc.edu (verdun.ks.uiuc.edu [130.126.120.129]) by havana.ks.uiuc.edu (8.9.1/8.9.1) with ESMTP id PAA10881; Tue, 6 Feb 2001 15:26:24 -0600 (CST) Received: from localhost (jim@localhost) by verdun.ks.uiuc.edu (8.9.3+Sun/8.9.1) with ESMTP id PAA07289; Tue, 6 Feb 2001 15:26:24 -0600 (CST) X-Authentication-Warning: verdun.ks.uiuc.edu: jim owned process doing -bs Date: Tue, 6 Feb 2001 15:26:23 -0600 (CST) From: Jim Phillips To: Hung-Chung Huang cc: CHEMISTRY@ccl.net Subject: Re: CCL:Two questions about MD and NAMD2.2! In-Reply-To: <3A804293.8080805@uh.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 6 Feb 2001, Hung-Chung Huang wrote: > 1. After I finished 60ps equilibration by using temperature > reassignment method (from 50K to 300K gradually) of NAMD2.2, the system > looked very stable around 300K (especially in the last 20ps of > equilibration). But why the system's temperature kept increasing after I > went to the MD phase simulations? P.S., I used temperature coupling , > Berendsen pressure bath coupling, and no PME. Did you set non-zero temperature coupling coefficients somewhere? If you don't do this, it will default to a column in your coordinates pdb file, which will probably be zero. This will result in none of the atom being coupled to the temperature bath. > 2. When I tried PME and if I positioned the ions (e.g. sodium ions) on > the edge of water box, the ions would leave the box and cause problems. > Is there any way to confine the sodium ions in the box (e,g., with > "wrapWater" on, waters can be wrapped back to another side of box if > they move out of the box)? Or what's the criterion to position ions > close to the protein for PME? The option wrapWater only effects output coordinates and is only there because visualizers are ignorant of the periodic cell. Your ions are diffusing between images, which is normal. What makes you say that your ions are causing problems? -Jim From chemistry-request@server.ccl.net Tue Feb 6 18:08:59 2001 Received: from changeofhabit.mr.itd.umich.edu (changeofhabit.mr.itd.umich.edu [141.211.144.17]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16N8xw27450 for ; Tue, 6 Feb 2001 18:08:59 -0500 Received: from U-Phar-carlsonh ([141.211.20.134]) by changeofhabit.mr.itd.umich.edu (8.9.3/3.2r) with ESMTP id SAA20370 for ; Tue, 6 Feb 2001 18:09:00 -0500 (EST) Date: Tue, 06 Feb 2001 18:13:44 -0500 From: "Heather A.Carlson" To: CHEMISTRY@ccl.net Subject: ADP in AMBER Message-ID: <2230681504.981483224@U-Phar-carlsonh> X-Mailer: Mulberry/2.0.0 (Win32) MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Content-Disposition: inline Hi All, I assume that there are AMBER parameters for ADP out there somewhere... I just can't find them. The parameterization protocol for AMBER uses RESP charges and doesn't end up being quite as "modular" as OPLS or CHARMM, so I don't think ADP is a simple derivative of the parameters available for nucleic acids. I very much appreciate any assistance in this quest. Thank you, Heather _________________________________________________________________________ Heather A. Carlson, Ph.D. John Gideon Searle Assistant Professor of Medicinal Chemistry http://www.umich.edu/~pharmacy/MedChem/faculty/carlson/ Assistant Professor of Chemistry http://www.umich.edu/~michchem/faculty/carlson/ University of Michigan Phone: (734) 615-6841 College of Pharmacy (2555 CCL) FAX: (734) 763-2022 428 Church Street E-mail: carlsonh@umich.edu Ann Arbor, MI 48109-1065 _________________________________________________________________________ From chemistry-request@server.ccl.net Tue Feb 6 14:44:44 2001 Received: from mail-b.bcc.ac.uk (mail-b.bcc.ac.uk [144.82.100.22]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f16Jiiw26572 for ; Tue, 6 Feb 2001 14:44:44 -0500 Received: from socrates-a.ucl.ac.uk by mail-b.bcc.ac.uk with SMTP (Mailer); Tue, 6 Feb 2001 19:44:42 +0000 From: uccatvm Message-Id: <28238.200102061944@socrates-a.ucl.ac.uk> Subject: summary: opls for tryptophan To: chemistry@ccl.net (CCL) Date: Tue, 6 Feb 2001 19:44:41 +0000 (GMT) X-Mailer: ELM [version 2.5 PL3] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi CCL'ers, Recently I asked the following question: ======================================================================= I am trying to get an OPLS potential for tryptophan. Jorgensen's paper on OPLS potential functions for proteins (W.L. Jorgensen, J. Tirado- Rives, J.Am.Chem.Soc. 110, 1657, 1988) contains OPLS parameters for tryptophan. According to the paper, standard geometries were used. However, I can't find standard values for all the tryptophan bond lengths and angles. Could someone give me a pointer where to find them? Secondly, as far as I am aware, there is no all-atom OPLS potential for tryptophan (the 1988 potential uses united atom CH groups). Is this correct? ======================================================================= Apparently, I was wrong about the non-availability of an all-atom OPLS potential for tryptophan. I would like to thank Daniel Price for pointing me to the supporting information belonging to Jorgensen et al.'s paper on the "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids" ,JACS 118, 11225-11236 (1996), and Willem P van Hoorn for pointing me to the information on Jorgensen's web site. I further want to thank Patrik Johansson for sending me his SCF/6-31G* geometry of tryptophan. Below are the replies from Daniel Price and Willem van Hoorn: Daniel Price: ============================= JACS (1996) 118:11225-11236 "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids" Supporting Information Non-bonded parameters (all-atom model) for all functionalities found in proteins are in the supporting information. Tryptophan is in Table 4. Also, under the heading Gas-phase structures: "The average differences between RHF/6-31G* and OPLS-AA results are 0.01 A for bond lengths, 2deg for bond angles and 1deg for dihedral angles." I would expect a 6-31G* minimization would yield an adequate geometry for rigid calculations. Bonded parameters are available for the entire OPLS-AA atom palette for flexible simulation as well. Willem van Hoorn: ============================= There definitely is an OPLS-AA force field for all protein residues. If you go to the Jorgensen group homepage (zarbi.chem.yale.edu) you can download the MCPRO manual and see for yourself. The exact geometries/parameters are not in there though... (you can find them in the MCPRO distribution). Best wishes, Tanja -- ==================================================================== Tanja van Mourik Royal Society University Research Fellow Chemistry Department University College London phone: +44 (0)20-7679-4663 20 Gordon Street e-mail: work: T.vanMourik@ucl.ac.uk London WC1H 0AJ, UK home: tanja@netcomuk.co.uk http://www.chem.ucl.ac.uk/people/vanmourik/index.html ==================================================================== From chemistry-request@server.ccl.net Tue Feb 6 20:22:10 2001 Received: from sundown.cs.cornell.edu (sundown.cs.cornell.edu [128.84.96.20]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f171MAw27905 for ; Tue, 6 Feb 2001 20:22:10 -0500 Received: from fafe.cs.cornell.edu (IDENT:avijit@fafe.cs.cornell.edu [128.84.97.167]) by sundown.cs.cornell.edu (8.9.3/8.9.3/R-3.2) with ESMTP id UAA10232 for ; Tue, 6 Feb 2001 20:22:10 -0500 (EST) Date: Tue, 6 Feb 2001 20:22:10 -0500 (EST) From: Avijit Ghosh X-Sender: To: Subject: CCL:GPL'd MD packages :: Summary Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I've extracted out the links into a compiled list as well as included the responses as a whole below that for some of the details w/ regards to particular programs. I've also added a few descriptors etc etc.. Here is the original question : --------------------original message---------------------------------- I was wondering whether anyone has any GPL'd code for MD? Particularly, whether there are any GPL'd force field implementations out there (I.E. MM*/OPLS*/AMBER* ). Cornell U. has a package (MOIL) here that is more or less public domain which includes an Amber88/(soon to be 95 implementation). There are a series of very nice programs that are available with source (NAMD/VMD from UIUC), Tinker from wustl (which is a really nice package btw) but is definitely copyrighted. However the licensing on these doesn't really encourage code reuse rather just personal code modification, and it would seem to me that code reuse might be beneficial in some circumstances rather than everyone reimplementing everyone elses algorithms/methods/force fields. In any case i'm curious as to what is out there already if anything. end-message---------------------------------------------------------------- Summary :: The programs below all have source, i've put the GPL'd code and GPLLike code at the top . I did some culling from the meta pages and put in some brief descriptions. As is hopefully obvious, don't trust me or my descriptions but take a look at the pages (links provided) for the real details. Hopefully this list will be useful to anyone who'd like to join incorporated their code into a GPL'd program and/or use algorithms from a gpl'd project. Apologies for all ytpos and any/all misrepresentations etc.. -Avi. Set (1) GPL'd Code. AMMP GPL MD Code (Apparantly has DFT incorporated!) http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html MOLDY GPL'd rigid body md http://www.earth.ox.ac.uk/~keith/moldy.html MOSCITO :: MD Code. ||ized. OPLS/AMBER/Gromacs. GPL'd http://ganter.chemie.uni-dortmund.de/~pas/moscito_info.html MMTK Open Sourced python based molecular modelling tool kit http://starship.python.net/crew/hinsen/MMTK/ Ghemical GPL Molecular modelling package http://www.uku.fi/~thassine/ghemical/ EGO_VIII || MD Code (GPL). http://www.lrz-muenchen.de/~heller/ego/egointro.html NAB :: Nucleic Acid Builder (implements amber95 :: has Generalized Born) (Free to do anything one would do w/ GPL :: see below) http://www.scripps.edu/case MPQC :: Massively Parallel Quantum Chemistry program. GPL'd. http://aros.ca.sandia.gov/~cljanss/mpqc/ ORAC MD for solvated biomolecules. GPL'd. http://www.chim.unifi.it:8080/orac/ Set two :: (soon to be) GPLish?? Allows redistribution?? CHIMP :: "generic tool for modelling of chemical phenomena." GPL'd. but "unavailable" ?? http://chimp.sourceforge.net/ GROMACS : || MD code . Being considered for GPL http://md.chem.rug.nl/~gmx NAMD :: || MD Code. "Licensee may redistribute without restriction works with up to 1/2 of their non-comment source code derived from at most 1/10 of the non-comment source code developed by Illinois and contained in the Software, provided that the above directions for notice and acknowledgement are observed." (see below) http://www.ks.uiuc.edu/Research/namd/ Cornell's Computational Biology TOOLS (Lots of free MD etc packages from R. Elber and H. Scheraga) :: Free for all use, as long as you don't sell it to people for $$. http://www.tc.cornell.edu/CBIO/ NWCHEM Massively || QM/MM code (free as long as you aren't a U.S. "baddy" ) http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html Set (3) Other. Many here are "Free for Academic use" which generally means no redistribution (Free use; no abuse :)), but as always look at the pages. Incidentally, free for academic use is nice but *imho* GPL (and friends or at least allowing redistribution) is nicer as it means i (and my friends) can try out your algorithm/force field/minimizer/integrator/solvation model etc etc w/ my (insert previous list in reverse order) and let others try it w/out having to reimplement each spoke on this wheel, which as far as I can gather pretty much everyone is doing. Tinker :: (Copyright WUSTL/Tinker but see below w/ regards using/redistributing source) http://dasher.wustl.edu/tinker/ DYNAMO :: F90 modules for QM/MM (OPLS-AA) free of charge. No redistribution. http://www.ibs.fr/ext/labos/LDM/projet6/welcome_fr.htm LAMMPS :: || MD code. Free for academic use. No redistribution. http://www.cs.sandia.gov/~sjplimp/lammps.html GULP :: simulation of periodic solids/clusters.. :: free for academics. no redist. http://www.ch.ic.ac.uk/gale/Research/gulp.html DL_POLY || MD code :: Free for Academic Scientists pursing non-commercial science. http://www.dl.ac.uk/TCSC/Software/DL_POLY/main.html ARTWork :: MD/MC code based on "Effective Medium Theory" , avail. for acad. purposes "as is" http://www.fysik.dtu.dk/~stoltze/artwork/artwork.html Autodock :: Docking code, free for academic use. http://www.scripps.edu/pub/olson-web/doc/autodock/ MDYNAMIX :: source code available (couldn't find license on web page) http://www.fos.su.se/physical/sasha/md_prog.html B :: Java based MD Code (couldn't find license on home page) http://www.scripps.edu/~nwhite/Biomer/index.html ------------------------------------------------------------------ Original responses :: ------------------------------------------------------------------ > From spoel@xray.bmc.uu.se Tue Feb 6 18:24:23 2001 Date: Thu, 1 Feb 2001 13:29:28 +0100 (CET) From: David van der Spoel To: Avijit Ghosh Subject: Re: CCL:GPL'd MD packages On Wed, 31 Jan 2001, Avijit Ghosh wrote: > > I was wondering whether anyone has any GPL'd code for MD? We are considering licensing GROMACS http://md.chem.rug.nl/~gmx under GPL. Right now we have a handful of developers using CVS. The code is definitely free (as in beer) for academics. One source of worry is the qulaity control. Obviously the results should be correct, and that means someone has to keep control over the source code. A linux kernel like model could be used for that. GROMACS is not (yet) very good in different forcefield (for proteins it is only GROMOS87 and GROMOS96, for small molecules one can write a topology manually or semi-automatically). However the code is *much* faster than anything else, and much easier to use due to our script-free (tm) user interface. So if you are interested in contributing force field wrappers to GROMACS you are more than welcome. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel Biomedical center, Dept. of Biochemistry s-mail: Husargatan 3, Box 576, 75123 Uppsala, Sweden e-mail: spoel@xray.bmc.uu.se www: http://zorn.bmc.uu.se/~spoel phone: 46 18 471 4205 fax: 46 18 511 755 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > From fparnold@chem.nwu.edu Tue Feb 6 18:24:29 2001 Date: Thu, 1 Feb 2001 08:11:17 -0600 (CST) From: Frederick P. Arnold Jr. To: Avijit Ghosh Subject: Re: CCL:GPL'd MD packages Hello, Moldy, from Keith Refeson at Oxford is GPL'd. It's a rigid-body, pair-potential based package, so it's not what you're looking for for biomolecules (probably), but you're certainly free to add whatever is missing. http://www.earth.ox.ac.uk/~keith/moldy.html you should probably also look at MMTK (Konrad Hinsen), which is a biomolecule forcefield. http://starship.python.net/crew/hinsen/MMTK/ There is, of course, the Ghemical project. Pretty raw at the moment, but with a nice minimalist builder and force-field. GPL'd, and we'd love to see some extra participation on making it a usable package. (my only contribution, regrettably, was rounding up a volunteer graduate student, and securing funding for an undergraduate programmer from Northwestern. Maybe someday I can start writing code again.) http://www.uku.fi/~thassine/ghemical/ Finally Tinker, while definitely copyrighted, is not onerously licensed (no worse than GAMESS-US). You know this, but maybe you should discuss wtih Jay Ponder what you want to use the code for. Similarly licensed, but higher-performance (if you have the hardware lying around), is NW-Chem > from PNL. (http://www.emsl.pnl.gov:2080) Designed for massively-parallel execution, and written in a mutant dialect of Fortran, it's still a pretty complete package, and not onerously licensed. -Fred Frederick P. Arnold, Jr. NUIT, Northwestern U. f-arnold@northwestern.edu > From bashtovyy@gmx.net Tue Feb 6 18:24:41 2001 Date: Thu, 1 Feb 2001 15:13:36 +0100 (MET) From: Denys Bashtovyy To: avijit@CS.Cornell.EDU Subject: GPL'd MD packages Hi Avijit, please, have a look at these: 1)AMMP http://www.cs.gsu.edu/~cscrwh/ammp/ammp.html 2)EGO_VIII http://www.lrz-muenchen.de/~heller/ego/egointro.html 3)Ghemical http://www.uku.fi/~thassine/ghemical/ 4)MMTK (is it under GPL?) http://dirac.cnrs-orleans.fr/programs/MMTK/index.html 5)Moldy http://www.earth.ox.ac.uk/~keith/moldy.html Best wishes, -- Denys Bashtovyy bashtovyy@gmx.net http://www.brc.hu/biophysics/memstruc.htm Sent through GMX FreeMail - http://www.gmx.net > From hutchisn@chem.nwu.edu Tue Feb 6 18:24:44 2001 Date: Thu, 1 Feb 2001 09:29:03 -0600 (CST) From: Geoff Hutchison To: Avijit Ghosh Subject: Re: CCL:GPL'd MD packages > copyrighted. However the licensing on these doesn't really encourage code > reuse rather just personal code modification, and it would seem to me > that code reuse might be beneficial in some circumstances rather than > everyone reimplementing everyone elses algorithms/methods/force fields. I am quite interested to hear if you get any responses. IMHO, it would be wonderful if more code was available under the GPL, which I personally think is quite useful for academic work. (For example, people could sell the code, but you could still get the source to see what's new.) Of course I'm a bit biased. I'm helping with the OELib/Babel 2.0 project, which is under GPL and the Ghemical molecular editor, which is also GPL'ed. The Ghemical source has a Tripos-like force field, but it's hardly a full implementation. -- -Geoff Hutchison Ratner Group (847) 491-3295 Northwestern Chemistry http://www.chem.northwestern.edu/ > From ponder@dasher.wustl.edu Tue Feb 6 18:24:46 2001 Date: Thu, 01 Feb 2001 09:42:47 -0600 From: Jay Ponder To: Avijit Ghosh Subject: Re: CCL:GPL'd MD packages Dear Avijit Ghosh, I saw your email to the CCL. Thanks for the mention of the TINKER package. I certainly want the TINKER code to be widely used, and I'm happy to have others modify the code for their own use. The problem with making the code "public domain" is at least two-fold. First, is the fact that for my own selfish purposes I want to have control of the future of the package. I've put many years of effort into getting the code to its current point, and if someone with greater bandwidth to the comp. chem. community came in and effectively took it over, I would be upset. Second, and less personal, it is very, very easy to break a code as complex as TINKER. We support multiple force fields and use some rather fancy algorithms for some things. I get submissions of code from other people all the time as possible additions to TINKER, and you would be amazed at the number of these that are fine for what they intend, but break some other aspect of the package. If TINKER were truly public domain, with lots of people hacking for their own purposes, I fear that it would quickly become a mass of incompatible and partially broken code. To the extent that TINKER is useful, it's because I and the folks in my very small group know every line of code and all the inevitable dependencies. The above said, I have allowed three groups to use TINKER in packages they redistribute: (1) TINKER is the force field engine in the GAMESS QM/MM implementation, (2) TINKER is the engine for the TINKERATE rate calculation package from Truhlar's group at the Univ. of Minnesota, and (3) TINKER's force field implementation, GB/SA solvation model and dynamics code is used with essentially no modification in Pande's Folding@Home distributed dynamics project at Stanford. I allowed these uses because I knew or knew of the people involved and I was fairly sure they would not break things, or allow their use of TINKER to get out of hand. (In that regard, I now sort of regret the Folding@Home use, since lots of Pande's users are non-chemist CS types who are horrified at the thought that Fortran code is running on their machines, want to rewrite the whole thing in C++, and generally have very little idea what they are getting into....). If you have some specific desired use for the TINKER code, please send me some email explaining. If, on the other hand, you simply think it would be "nice" if their were a GPL'd dynamics package, I would reply that I'm not sure the world is ready to deal with that yet--the science behind the codes is not yet mature enough to be ossified into generic public domain packages. Best wishes, Jay P. -- Jay W. Ponder Phone: (314) 362-4195 Biochemistry, Box 8231 Fax: (314) 362-7183 Washington University Medical School 660 South Euclid Avenue Email: ponder@dasher.wustl.edu St. Louis, Missouri 63110 USA WWW: http://dasher.wustl.edu/ > From case@scripps.edu Tue Feb 6 18:25:16 2001 Date: Thu, 1 Feb 2001 10:23:19 -0800 From: David Case To: Avijit Ghosh Cc: CHEMISTRY@ccl.net Subject: Re: CCL:GPL'd MD packages On Wed, Jan 31, 2001, Avijit Ghosh wrote: > > I was wondering whether anyone has any GPL'd code for MD? > Particularly, whether there are any GPL'd force field > implementations out there (I.E. MM*/OPLS*/AMBER* ). NAB (Nucleic acid builder) implements the Amber95 force field. It includes generalized Born calculations, but *not* periodic boundary conditions simulations, so it may or may not satisfy particular needs. In spite of the name, it is designed to work on proteins as well as nucleic acids. Whether or not the code itself (mainly in file sff.c) would be useful to transfer to other applications is of course a subjective decision, but you are certainly free to do anything allowed by the terms of GPL. See my web page (below) for more info. ....good luck...dac -- ================================================================== David A. Case | e-mail: case@scripps.edu Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | http://www.scripps.edu/case ================================================================== > From czarek@scheraga2.chem.cornell.edu Tue Feb 6 18:25:31 2001 Date: Thu, 1 Feb 2001 18:04:08 -0500 (EST) From: Cezary Czaplewski To: Avijit Ghosh Subject: Re: CCL:GPL'd MD packages You can look at http://sal.kachinatech.com/Z/2/index.shtml Some of MD programs listed there are released under GPL but I have never tryied personally any of them. czarek > From Keith.Refson@earth.ox.ac.uk Tue Feb 6 18:25:48 2001 Date: Mon, 5 Feb 2001 09:45:49 +0000 From: Keith Refson Subject: CCL:GPL'd MD packages Resent-Date: Mon, 5 Feb 2001 09:47:25 GMT Resent-From: Keith Refson Resent-To: Computational Chemistry List CCL You will find links several MD packages on http://zeus.polsl.gliwice.pl/~nikodem/linux4chemistry.html However only a few are GPLed. I would have expected that the GPL be adopted more widely in science than it has been, since it is pretty much an expression of the purest ideals of freely sharing knowledge. However it seems that the constant pressure for cash is stifling these ideals. Keith Refson -- Dr Keith Refson, "Paradigm is a word too often used by those who would Dept of Earth Sciences like to have a new idea but cannot think of one." Parks Road, -- Mervyn King, Deputy Governor, Bank of England Oxford OX1 3PR, UK Keith.Refson@ Tel: 01865 272026 earth.ox.ac.uk Fax: 01865 272072 -= 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 jim@ks.uiuc.edu Tue Feb 6 19:54:40 2001 Date: Thu, 1 Feb 2001 10:03:32 -0600 (CST) From: Jim Phillips To: Avijit Ghosh Subject: Re: CCL:GPL'd MD packages Hi, Depending on your definition of reuse, you may find this clause in the NAMD/VMD licenses relevant (read the whole license, though): Licensee may redistribute without restriction works with up to 1/2 of their non-comment source code derived from at most 1/10 of the non-comment source code developed by Illinois and contained in the Software, provided that the above directions for notice and acknowledgement are observed. Any other distribution of the Software or any derivative work requires a separate license with Illinois. Licensee may contact Illinois (namd@ks.uiuc.edu) to negotiate an appropriate license for such distribution. http://www.ks.uiuc.edu/Research/namd/license.html -Jim On Wed, 31 Jan 2001, Avijit Ghosh wrote: > > I was wondering whether anyone has any GPL'd code for MD? > Particularly, whether there are any GPL'd force field > implementations out there (I.E. MM*/OPLS*/AMBER* ). Cornell U. has a > package (MOIL) here that is more or less public domain which includes an > Amber88/(soon to be 95 implementation). There are a series of > very nice programs that are available with source (NAMD/VMD from UIUC), > Tinker from wustl (which is a really nice package btw) but is definitely > copyrighted. However the licensing on these doesn't really encourage code > reuse rather just personal code modification, and it would seem to me > that code reuse might be beneficial in some circumstances rather than > everyone reimplementing everyone elses algorithms/methods/force fields. > > In any case i'm curious as to what is out there already if > anything. > > -Avi > > (W/ apologies about fomenting the Fortran/C++ war into a source > code licensing war :) ) > > Actually w/ regards to programming languages, let me mention that I did > my undergrad. in CS and at the time we did every class (except for > operating systems) in Pascal which isn't obviously "useful". Really, > language doesn't matter; you can write equally crap/unmaintainable code > in all! :) > > > > -= 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 > > > > > >