From chemistry-request@server.ccl.net Sat Jul 20 11:43:04 2002 Received: from buffy.cs.uoguelph.ca ([131.104.96.176]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6KFh3B07171 for ; Sat, 20 Jul 2002 11:43:03 -0400 Received: from smith ([131.104.32.146]) by buffy.cs.uoguelph.ca (8.11.6/8.11.6) with ESMTP id g6KFh3e05777 for ; Sat, 20 Jul 2002 11:43:03 -0400 (EDT) From: "Bill Smith" Organization: Math & Stats, University of Guelph To: chemistry@ccl.net Date: Sat, 20 Jul 2002 11:42:11 -0400 MIME-Version: 1.0 Content-type: text/enriched; charset=US-ASCII Content-transfer-encoding: 7BIT Subject: Re: CCL:Equilibrium constants Message-ID: <3D394C93.2969.35AB18B@localhost> Priority: normal In-reply-to: <3D38AB58.453C1A18@georgetown.edu> X-mailer: Pegasus Mail for Win32 (v3.12c) 0100,0100,0100ArialApart from standard tables like the JANAF Tables (CHASE, M., Jr., 1998, {\it NIST-JANAF Thermochemical Tables, 4th ed., J. Phys. and Chem. Reference Data Monograph No. 9,} (Am.Chem. Society, Am. Inst. PhysicsCourier New).ArialData , you can get a lot of this data from the free Lite version of the reaction equilibrium software package EQS4WIN, available at http://www.mathtrek.com Arial CEOn 19 Jul 2002, at 20:14, knauerc wrote: 7F00,0000,0000> Does anyone know where I can find good data for the equilibrium > constants, (as a function of temperature), for the reactions: > > H2 + Cl2 = 2HCL > > and > > H2 + Br2 = 2HBr > > Thank you. > > Connie Knauer > Georgetown University > knauerc@georgetown.edu > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To > Admins Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | > Jan: jkl@ccl.net > > > > From chemistry-request@server.ccl.net Fri Jul 19 21:12:56 2002 Received: from ce.fis.unam.mx ([132.248.33.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6K1CtB07206 for ; Fri, 19 Jul 2002 21:12:55 -0400 Received: from venus.fis.unam.mx ([132.248.33.20]) by ce.fis.unam.mx (8.11.2/8.11.2) with ESMTP id g6K1OTR16497 for ; Fri, 19 Jul 2002 20:24:29 -0500 Message-Id: <5.1.0.14.0.20020719201125.00a5ed80@pop3.norton.antivirus> X-Sender: ramon/ce.fis.unam.mx@pop3.norton.antivirus X-Mailer: QUALCOMM Windows Eudora Version 5.1 Date: Fri, 19 Jul 2002 20:13:22 -0500 To: chemistry@ccl.net From: =?iso-8859-1?Q?Ram=F3n?= =?iso-8859-1?Q?_Gardu=F1o-Ju=E1rez?= Subject: SAW for protein lattice models Mime-Version: 1.0 Content-Type: multipart/alternative; boundary="=====================_33505109==_.ALT" X-MailScanner: Found to be clean --=====================_33505109==_.ALT Content-Type: text/plain; charset="iso-8859-1"; format=flowed Content-Transfer-Encoding: quoted-printable Dear CCLers: I am designing a molecular modeling course for next semester. One of the=20 key topics I am planning to include is the Self Avoiding Walk algorithm use in modeling HP= =20 toy protein models. I have a collection of several computer programs, some I have written=20 myself like Genetic Algorithms, Simulated Annealing, Molecular Mechanics and others, but=20 nothing on SAW. I am wondering if any of you have written a computer program that can do=20 this for 2D and 3D, and that is willing to share. For teaching purposes I will appreciate a=20 FORTRAN code but C or C++ is also welcomed. Much obliged, Ram=F3n Gardu=F1o P.S. Please reply directly to me. "Everything is lost when bad people are subject of praise and the good people are subject= =20 of muckery" "Todo est=E1 perdido cuando los malos sirven de= ejemplo y los buenos de mofa" Dem=F3crates ___________________________________________________________________________ Dr. Ram=F3n=20 Gardu=F1o-Ju=E1rez Research Professor= =20 in Biophysics CENTRO DE CIENCIAS FISICAS | EMAIL: ramon@fis.unam.mx UNIVERSIDAD NAL. AUTONOMA DE MEXICO | Apdo. Postal 48-3 |=20 VOICE: +52(55)56227749; +52(777)3291749 62251 Cuernavaca, Morelos | MEXICO |= =20 FAX: +52(55)56227775; +52(777)3291775 __________________________________EOF ____________________________________ = =20 --=====================_33505109==_.ALT Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear CCLers:

I am designing a molecular modeling course for next semester. One of the key topics I am
planning to include is the Self Avoiding Walk algorithm use in modeling HP toy protein models.
I have a collection of several computer programs, some I have written myself like Genetic
Algorithms, Simulated Annealing, Molecular Mechanics and others, but nothing on SAW.

I am wondering if any of you have written a computer program that can do this for 2D and 3D,
and that is willing to share. For teaching purposes I will appreciate a FORTRAN code but C
or C++ is also welcomed.

Much obliged,

Ram=F3n Gardu=F1o

P.S. Please reply directly to me.

          &= nbsp;       "Everything is lost when bad people are subject of praise
         =           &= nbsp;          &nb= sp;            and the good people are subject of muckery"
          &= nbsp;           "Todo est=E1 perdido cuando los malos sirven de ejemplo
         =           &= nbsp;         &n= bsp;         &nb= sp;        y los buenos de mofa"
        &n= bsp;         &nb= sp;         &nbs= p;          = ; 
            &nbs= p;            &n= bsp;            =             &nbs= p;     Dem=F3crates
__________________________________________________________________= _________
            &nbs= p;            &n= bsp;            =             &nbs= p;     Dr. Ram=F3n Gardu=F1o-Ju=E1rez
            &nbs= p;            &n= bsp;            =             &nbs= p;    Research Professor in Biophysics
CENTRO DE CIENCIAS FISICAS           &nb= sp;            | EMAIL: ramon@fis.unam.mx
UNIVERSIDAD NAL. AUTONOMA DE MEXICO |
Apdo. Postal 48-3            =             &nbs= p;            &n= bsp;             | VOICE: +52(55)56227749; +52(777)3291749
62251 Cuernavaca, Morelos           &nb= sp;            &= nbsp;       |
MEXICO           &nbs= p;            &n= bsp;            =             &nbs= p;            &n= bsp;     | FAX:   +52(55)56227775; +52(777)3291775
__________________________________EOF ____________________________________   --=====================_33505109==_.ALT-- From chemistry-request@server.ccl.net Sat Jul 20 14:41:50 2002 Received: from ns0.scripps.edu ([192.42.82.58]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6KIfiB10972 for ; Sat, 20 Jul 2002 14:41:48 -0400 Received: from antigen.scripps.edu (antigen.scripps.edu [137.131.200.100]) by ns0.scripps.edu (8.11.6/TSRI-4.2rx) with SMTP id g6KIfcq29502 for ; Sat, 20 Jul 2002 11:41:38 -0700 (PDT) Received: from relay2.scripps.edu(137.131.200.30) by antigen.scripps.edu via csmap id 7718; Sat, 20 Jul 2002 11:35:10 -0700 (PDT) Received: from goliath.scripps.edu (goliath.scripps.edu [137.131.108.88]) by relay2.scripps.edu (8.11.6/TSRI-4.2.1rAV) with ESMTP id g6KIfFO15506; Sat, 20 Jul 2002 11:41:15 -0700 (PDT) Received: from aaron (aaron [137.131.108.91]) by goliath.scripps.edu (SGI-8.9.3/TSRI-3.0.1) with SMTP id LAA25095; Sat, 20 Jul 2002 11:41:15 -0700 (PDT) Message-Id: <200207201841.LAA25095@goliath.scripps.edu> Date: Sat, 20 Jul 2002 11:41:13 -0700 (PDT) From: Michel Sanner Reply-To: Michel Sanner Subject: Re: CCL:Problem with ADT (fwd) To: a_juanphd@yahoo.com, smolnar@jadeinc.com Cc: garrett@scripps.edu, stoffler@scripps.edu, gillet@scripps.edu, lindy@scripps.edu, rhuey@scripps.edu, chemistry@ccl.net MIME-Version: 1.0 Content-Type: TEXT/plain; charset=us-ascii Content-MD5: jOZxYe+2WZ/Hzr7Lyvvq2g== X-Mailer: dtmail 1.3.0 @(#)CDE Version 1.4.2 SunOS 5.8 sun4u sparc Hello, The message "polygon offset extension failed" is not an error message but rather a warning message that your OpenGL implementation does not implement offset polygons. This extension is not used explicitly in ADT, but DejaVu (the underlying visualization component ) checks for its implementation because it can be used to outline the boundaries of triangles by drawing lines on top of a Gouraud or flat shaded surface (i.e. solide surface). We will stop printing this message (which is really just a debugging message). Thank you for pointing this out to us :) -Michel > ---------- Forwarded message ---------- > Date: Thu, 18 Jul 2002 19:10:18 -0700 (PDT) > From: amor san juan > To: "Stephen P. Molnar, Ph.D." , chemistry@ccl.net > Subject: CCL:Problem with ADT > > Dear Dr. Molnar: > > I have the same problem. The platform I installed ADT > is RedHat7 linux and everytime I run the program ADT > > > I run the control distributed file 3ptb-ben and it > generated ben.pdbq & 3ptb.pdbqs almost perfectly. Now, > I'm trying to resolve usage of ADT with my samples. > > Anyone would please kindly give us hint. > > Sincerely, > Amor San Juan > University of the Philippines-Diliman > > --- "Stephen P. Molnar, Ph.D." > wrote: > > Clueless in Columbus - starting AutoDock Tools. > > I've installed > > complete1.5_i86Linux2_acad.tar.Z. When I start adt, > > after sourcing > > install.bash, I get the message: > > > > 'polygonOffset extension FAILED' > > > > I would assume this is a python error, as adt, seems > > to work,. but my > > question is what have I failed to install? > > > > I am running the SuSE v7.1 Linux distribution. > > > > Thanks in advance. > > > > > > > > -= This is automatically added to each message by > > mailing script =- > > CHEMISTRY@ccl.net -- To Everybody | > > CHEMISTRY-REQUEST@ccl.net -- To Admins > > Ftp: ftp.ccl.net | WWW: > > http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > > > > > > > > > __________________________________________________ > Do You Yahoo!? > Yahoo! Autos - Get free new car price quotes > http://autos.yahoo.com > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > ----------------------------------------------------------------------- Michel F. Sanner Ph.D. The Scripps Research Institute Assistant Professor Department of Molecular Biology 10550 North Torrey Pines Road Tel. (858) 784-2341 La Jolla, CA 92037 Fax. (858) 784-2860 sanner@scripps.edu http://www.scripps.edu/sanner ----------------------------------------------------------------------- From chemistry-request@server.ccl.net Sun Jul 21 07:08:40 2002 Received: from web12808.mail.yahoo.com ([216.136.174.43]) by server.ccl.net (8.11.6/8.11.0) with SMTP id g6LB8eB12062 for ; Sun, 21 Jul 2002 07:08:40 -0400 Message-ID: <20020721110839.393.qmail@web12808.mail.yahoo.com> Received: from [203.87.150.242] by web12808.mail.yahoo.com via HTTP; Sun, 21 Jul 2002 04:08:39 PDT Date: Sun, 21 Jul 2002 04:08:39 -0700 (PDT) From: amor san juan Subject: Energy minimization To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hello, What are the good minimization algorithms for up to 150max atoms? My goal to this most stable energy conformer is to use it in docking experiment. I tried MM3 & MMFF94 algorithms built in a specific commercial software. Results showed that none of the minimized structures in synchronized with ben.pdbq distributed file in AutoDock. Im calling the attention of Autodock users, have you encountered this problem? Kindly give me a hint. I would also appreciate if someone would be considerate to give me good reading materials about energy minimization. Thanks, Amor __________________________________________________ Do You Yahoo!? Yahoo! Health - Feel better, live better http://health.yahoo.com From chemistry-request@server.ccl.net Sun Jul 21 12:14:37 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6LGEa320282 for ; Sun, 21 Jul 2002 12:14:37 -0400 Received: from eden.rutgers.edu (er3.rutgers.edu [165.230.180.141]) by goshen.rutgers.edu (Postfix) with ESMTP id 19ECB23E16 for ; Sun, 21 Jul 2002 12:10:41 -0400 (EDT) Received: by eden.rutgers.edu (Postfix, from userid 37805) id D7B6415E7F; Sun, 21 Jul 2002 12:10:30 -0400 (EDT) Date: Sun, 21 Jul 2002 12:10:30 -0400 (EDT) From: Jianquan Chen X-Sender: jianquan@er3.rutgers.edu To: chemistry@ccl.net Subject: summary on Convert 2d to 3d in batch mode In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Tue, 4 Jun 2002 12:11:52 -0400 (EDT) From: Jianquan Chen To: chemistry@ccl.net Subject: CCL:convert 2d to 3d Hi, I need to convert thousands of 2d sdf file to 3d mol2 files and add charges. But I met a problem. Concord and Corina is too expensive. Concord is built in the alchemy2000 that is not very expensive. I have a question before I buy Alchemy2000. Can I run Alchemy2000 in batch mode? I mean, can I use alchemy2000 to convert thousands of 2d file to 3d automatically. Thank you in advance. jianquan chen A>>>From: Anselm Horn To: Jianquan Chen Subject: Conversion + charges Hi, some time ago, we computed the complete Maybridge database (ca. 53.000 compounds) using semiempirical MO-theory (with geometry optimization) starting from 2D structures. We used Corina for the conversion step, because it may easily used in batch mode. So, this is my recommendation. Concerning your charge problem: If you just neeed *any* charges, you could also try Gasteiger-Marsili. Unfortunately, I don't know, if there's a free tool around to calculate those. If you want to do that with Mopac, you simply do a single energy calculation - add keyword 1SCF to the keyword line. Although Dave Gallagher told you of the new Mopac features, I guess that you use the old but free version of Mopac. There is no linear scaling technique implemented in that version. So, how many molecules (which size) do you intend to compute? Regards, B>>>From: Karl Irikura To: Jianquan Chen Subject: Re: CCL:convert 2d to 3d Hi Jianquan. I don't know what Concord is, but I've used Alchemy2000 to convert 2D MOL files to 3D in batch mode. It's a good idea to inspect the final 3D structures, especially if stereochemistry is important. I did this a few years ago for a few thousand structures (for the NIST WebBook, webbook.nist.gov), including geometry optimization at the PM3 level. Good luck! Karl I. C>>>From: skillman@eyesopen.com To: Jianquan Chen Subject: Re: CCL:convert 2d to 3d Jianquan- Are you really at rutgers? Are you working on academic pursuits without ties to industry? If so, our software (omega does 2d sdf to multi-conformer (or single conf) 3dmol2 and we also have gasteiger charges etc) is free to academics working on academic projects. www.eyesopen.com Cheers, Geoff D>>>From: Wolf-Dietrich Ihlenfeldt To: Jianquan Chen Subject: Re: CCL:convert 2d to 3d Hello, I suggest you talk to the CORINA people directly. If you are at an university, I am sure things can be arranged. As a starter, there is a free email batch service (send your structures by email and get the structures back overnight) somewhere at www2.ccc.uni-erlangen.de/services/ From chemistry-request@server.ccl.net Sun Jul 21 12:16:20 2002 Received: from goshen.rutgers.edu ([165.230.180.150]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6LGGK320309 for ; Sun, 21 Jul 2002 12:16:20 -0400 Received: from eden.rutgers.edu (er3.rutgers.edu [165.230.180.141]) by goshen.rutgers.edu (Postfix) with ESMTP id A62C61FE1A for ; Sun, 21 Jul 2002 12:14:08 -0400 (EDT) Received: by eden.rutgers.edu (Postfix, from userid 37805) id 80CB015E7F; Sun, 21 Jul 2002 12:14:08 -0400 (EDT) Date: Sun, 21 Jul 2002 12:14:08 -0400 (EDT) From: Jianquan Chen X-Sender: jianquan@er3.rutgers.edu To: chemistry@ccl.net Subject: summary on adding charges to thousands of molecule via MOPAC In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII original question is: Hi, I need to add charge to thousands of molecules. MOPAC is free but slow and sometimes changes the moleucular structure. I don't know how MOPAC works. I have 2 questions. Can I run MOPAC without optimizing the molecular structure? Is there any way to accelate MOPAC? I don't need very accurate charges. Thanks a lot for any response. Jianquan Chen Hi Jianquan A>>>>> Reply From David Gallagher, Fujitsu 1. MOPAC can run just an "SCF" which does not change the geometry. This is the fastest way to get partial charges. 2. The new linear-scaling versions of MOPAC can calculate up to 20,000 atoms in just a few hours on a Windows desktop computer. With "MOPAC 2002", an SCF on a 641 atom protein takes about 3 minutes on a 1000 MHz Pentium III. There is more information at http://www.cachesoftware.com/mopac/index.shtml David Gallagher, Fujitsu B>>>>Reply From David Gallagher, Fujitsu 1. MOPAC can run just an "SCF" which does not change the geometry. This is the fastest way to get partial charges. 2. The new linear-scaling versions of MOPAC can calculate up to 20,000 atoms in just a few hours on a Windows desktop computer. With "MOPAC 2002", an SCF on a 641 atom protein takes about 3 minutes on a 1000 MHz Pentium III. There is more information at http://www.cachesoftware.com/mopac/index.shtml David Gallagher, Fujitsu C>>>>From: Jolanta Latosinska Subject: Re: CCL:calculate charge using MOPAC Dear Chen, You can run one scf within mopac package. You should type "0" instaed of "1" after each parameter. Concerning the speed - try more recent version. JL D>>>From: Anselm Horn To: Jianquan Chen Subject: Conversion + charges Hi, some time ago, we computed the complete Maybridge database (ca. 53.000 compounds) using semiempirical MO-theory (with geometry optimization) starting from 2D structures. We used Corina for the conversion step, because it may easily used in batch mode. So, this is my recommendation. Concerning your charge problem: If you just neeed *any* charges, you could also try Gasteiger-Marsili. Unfortunately, I don't know, if there's a free tool around to calculate those. If you want to do that with Mopac, you simply do a single energy calculation - add keyword 1SCF to the keyword line. Although Dave Gallagher told you of the new Mopac features, I guess that you use the old but free version of Mopac. There is no linear scaling technique implemented in that version. So, how many molecules (which size) do you intend to compute? Regards, E>>>From: "Thomas [iso-8859-1] Hnbner" To: Jianquan Chen Subject: Re: CCL:calculate charge using MOPAC Hello, your first question about doing charge calculations in Mopac without optimizing has already been answered earlier, although I would not really recommend it. A faster method to calculate charges is the one called Gasteiger, which is for example implemented in the Vega package among others like Insight, Sybyl e.a.. A new release of Vega was just announced on CCL by Giulio Vistoli a few messages earlier, see also http://users.unimi.it/~dd. Together with Babel you should be able to come from almost any file format and generate Gasteiger charges for your molecules. The ViewerLite from Accelrys can calculate charges as well, probably also via a Gasteiger look alike. One word of caution though, Gasteiger is mainly applied to standard organic/medicinal molecules, and thus probably only validated for that class of compounds. A fuzzy clasification, I know ;-). Once you leave the field of standard chemistry, you should use a quantum chemical method like Mopac, or if it gets even worse you have to revert to first principle methods like DFT or HF, as in Gaussian (commercial) or Gamess (free). Bye Thomas F>>>From: eric.vangrevelinghe@netcourrier.com To: jianquan@eden.rutgers.edu Cc: chemistry@ccl.net Dear Jianquan, You should take a look on the BatchMan program: http://web.univ-orleans.fr/SCIENCES/ICOA/batchman/index.html BatchMan is a FREE graphic interface to Mopac, Gamess and Babel, mainly oriented to handle a large number of structures (batch mode). With the use of one SCF step in the mopac calculation (chose optimization: none in the Mopac keywords interface), you will be able to treat easily several thousand of structures without the need to know how Mopac works. Hope that helps. Regards, Eric. G>>>From: Juan Alexander Padron Garcia To: Jianquan Chen Subject: Re: CCL:calculate charge using MOPAC [ The following text is in the "iso-8859-1" character set. ] [ Your display is set for the "US-ASCII" character set. ] [ Some characters may be displayed incorrectly. ] Dear Chen: Yes, you may. To skip the geometry optimization just add the keyword "1SCF". The acceleration is not that easy and is not required if you use the 1SCF command. Sometimes the use of the Eigenvector Following (EF keyword) reduce the calculation times. But a simple command line like "1SCF PM3 MMOK GEO-OK" should work. Additionally, if you need help making a batch of thousand structures I can give you an small MSDOS program I wrote that do so automatically. From chemistry-request@server.ccl.net Sun Jul 21 21:52:05 2002 Received: from smtp1.dti.ne.jp ([202.216.228.36]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g6M1q4310863 for ; Sun, 21 Jul 2002 21:52:04 -0400 Received: from b159504364 (PPP249.fukuoka-ip.dti.ne.jp [211.132.92.249]) by smtp1.dti.ne.jp (3.07) with SMTP id g6M1pxmg007867 for ; Mon, 22 Jul 2002 10:52:02 +0900 (JST) Message-ID: <001101c23122$578861c0$f95c84d3@b159504364> From: "Telkuni" To: Subject: Force Fields of MM Date: Mon, 22 Jul 2002 10:51:47 +0900 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-2022-jp" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 Dear CCLers, I'm a novice of Molecular Mechanics. I like to know the features of each MM force field (Amber, UFF and so on...) Could you teach me the strong and weak points of each force field? ---------------------------------------------- Telkuni Tsuru Kyushyu Electronic Technology and Research telkuni@venus.dti.ne.jp ----------------------------------------------