From chemistry-request@server.ccl.net Thu Nov 29 03:05:09 2001 Received: from sina.com ([202.108.35.239]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAT859B05883 for ; Thu, 29 Nov 2001 03:05:09 -0500 Received: (qmail 23417 invoked by uid 99); 29 Nov 2001 08:03:56 -0000 Message-ID: <20011129080356.23416.qmail@sina.com> From: t218gy To: chemistry@ccl.net Subject: About UHF's spectral explaining MIME-Version: 1.0 Date: Thu, 29 Nov 2001 16:03:56 +0800 X-Mailer: SinaMail 3.0Beta (FireToad) X-Priority: 3 Dear sir, I encounter a problem that the RHF of ground state is unstable, thus I employ the UHF to get the conformation. Now my question is whether I could use this value to compare with the UV/visible/near-IR spectra and how I fulfill it. Thanks ______________________________________ =================================================================== 新浪免费电子邮箱 (http://mail.sina.com.cn) 新浪分类信息：轻松订阅，量身定制！周周有礼，大奖等你！ (http://classad.sina.com.cn/) 七种手机图片、千首铃声下载……新浪短信无限精彩! (http://sms.sina.com.cn/) From chemistry-request@server.ccl.net Thu Nov 29 03:15:52 2001 Received: from mh1-munich.munich.accelrys.com ([192.190.183.254]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAT8FqB06054 for ; Thu, 29 Nov 2001 03:15:52 -0500 Received: from woernitz.munich.accelrys.com ([172.29.64.178] helo=woernitz.munich.msi-eu.com) by mh1-munich.munich.accelrys.com with esmtp (Exim 3.12 #1 (Debian)) id 169MMA-0007pI-00; Thu, 29 Nov 2001 09:15:42 +0100 Received: (from jxh@localhost) by woernitz.munich.msi-eu.com (8.8.8/8.8.8) id JAA04911; Thu, 29 Nov 2001 09:15:42 +0100 (MET) From: "Joerg-Ruediger Hill" Message-Id: <10111290915.ZM4907@woernitz.munich.msi-eu.com> Date: Thu, 29 Nov 2001 09:15:41 +0100 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: scerri@chem.ucla.edu, CHEMISTRY@ccl.net Subject: collation of responses on ab initio/first principles Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="PART-BOUNDARY=.110111290915.ZM4907.munich.msi-eu.com" --PART-BOUNDARY=.110111290915.ZM4907.munich.msi-eu.com Content-Description: Text Content-Type: text/plain ; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable X-Zm-Decoding-Hint: mimencode -q -u > I was not so much interested in the origin of the term ab initio but > of course the answers are interesting. My real aim was to discover > whether there is an intended subtle shift in meaning in using "first > principles" rather than ab initio. None of the responses indicate > that this might be so. In my understanding there has always been that subtle shift in meaning you talk about and others seem to think the same: "The appealing feature of the LDA approach is that it treats both exchang= e and correlation effects on an equal footing and requires only to solve one-particle equations with a local effective potential. Its limitation is that the exact potential is not available and one is forced to work with expressions transferred from simple model systems. This brings an empirical element in such calculations, although they avoid adjustable parameters. Therefore, a clear distinction in terminology seems desireabl= e between the exact-exchange 'HF plus electron correlation' approach on the= one hand and the LDA or LSD-based approaches on the other hand. The forme= r are known as 'ab initio' methods, while for the latter the terminus 'firs= t principle' method is widely accepted. Perhaps it is better to be more specific and refer directly to the 'density functional' (DF) or to the 'local (spin) density approximation' (LDA, LSD)." J. Sauer, Chem. Rev. (1989), 89, 199. > Also, I was particularly interested in the posting from Per Ola > Norrby who discusses how basis sets are constructed in a > semi-empirical manner especially regarding expansion coefficients and > contraction. I would be interested in learning more about this > aspect and/or references to where it is discussed in the literature. > >> It's not always realised that what is called "ab initio" incorporates= >> many empirical parameters. For example, a standard HF/6-31G* calculat= ion >> would be called "ab initio", but all the exponents and contraction >> coefficients in the basis set were selected by fitting to >> experimental data! That's one of the main reasons for the success of >> the Pople basis sets, they have been fit to real data, thus they are >> good at reproducing real data. The effect, of course, is that the >> basis set incorporates systematical errors that to a large extent >> cancels the systematical errors in HF ... Basis sets are NOT constructed in a "semi-empirical manner" or "fitted to experimental data". Basis sets are obtained by performing electronic structure calculations (Hartree-Fock, MP2, DFT - the method the basis set= is to be used with) usually for atoms but sometimes for molecules while varying the exponents of the basis functions and the expansion coefficien= ts until the minimum energy has been found. Basis sets obtained for Hartree-= Fock are often transferred to other electronic structure methods which usually gives good results. See e.g.: - basics, including the derivation of Pople's basis sets S. Huzinaga, Computer Physics Reports (1985), 2, 279 - more recent developments in basis sets for Hartree-Fock A. Sch=E4fer, H. Horn and R. Ahlrichs, J. Chem. Phys. (1992), 97, 2571 - basis sets for DFT N. Godbout, D. R. Salahub, J. Andzelm and E. Wimmer, Can J. Chem. (1992),= 70, 560 You might also want to read about the work of T. H. Dunning, Jr. concerni= ng correlation-consistent basis sets. J=F6rg-R=FCdiger Hill -- = -------------------------------------------------------------------------= ----- Dr. J=F6rg-R=FCdiger Hill | Phone +49 89 61459-413 | The opinions exp= ressed in Accelrys GmbH | Fax +49 89 61459-400 | this message are my= per- Inselkammerstrasse 1 | E-mail jxh@accelrys.com | sonal opinions an= d no D-82008 Unterhaching | | offical statements= of Germany | http://www.accelrys.com/ | Accelrys Inc. -------------------------------------------------------------------------= ----- --PART-BOUNDARY=.110111290915.ZM4907.munich.msi-eu.com-- From chemistry-request@server.ccl.net Wed Nov 28 23:15:54 2001 Received: from web14914.mail.yahoo.com ([216.136.225.241]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fAT4FrB31049 for ; Wed, 28 Nov 2001 23:15:53 -0500 Message-ID: <20011129041547.20667.qmail@web14914.mail.yahoo.com> Received: from [161.142.10.27] by web14914.mail.yahoo.com via HTTP; Wed, 28 Nov 2001 20:15:47 PST Date: Wed, 28 Nov 2001 20:15:47 -0800 (PST) From: Ng Pei Ling Subject: HETATM To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="0-1453715572-1007007347=:20462" --0-1453715572-1007007347=:20462 Content-Type: multipart/alternative; boundary="0-33698974-1007007347=:20462" --0-33698974-1007007347=:20462 Content-Type: text/plain; charset=us-ascii I'm a master student in USM , Malaysia. I'm doing on project about molecule quercetin bind with macromolecule of enzyme cancer. I check on the binding affinity of molecule flavonoids to enzyme cancer. I find HETATM in my Protein Data Bank file. But, I don't know what is the meaning of HETATM file. May I know the answer of below question ? 1. What are HETATM ? What are they mean ? 2. What are the meaning of the fourth and fifth row value in Protein Data Bank file? Please refer to attached file. Thanks. --------------------------------- Do You Yahoo!? Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. --0-33698974-1007007347=:20462 Content-Type: text/html; charset=us-ascii

I'm a master student in USM , Malaysia. I'm doing on project about molecule quercetin bind with macromolecule of enzyme cancer. I check on the binding affinity of molecule flavonoids to enzyme cancer. I find HETATM in my Protein Data Bank file. But, I don't know what is the meaning of HETATM file. May I know the answer of below question ?

1. What are HETATM ? What are they mean ?

2. What are the meaning of the fourth and fifth row value in Protein Data Bank file? Please refer to attached file. Thanks.


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GeoCities - quick and easy web site hosting, just $8.95/month. --0-33698974-1007007347=:20462-- --0-1453715572-1007007347=:20462 Content-Type: application/msword; name="HETATM Que.doc" Content-Transfer-Encoding: base64 Content-Description: HETATM Que.doc Content-Disposition: attachment; filename="HETATM Que.doc" 0M8R4KGxGuEAAAAAAAAAAAAAAAAAAAAAPgADAP7/CQAGAAAAAAAAAAAAAAAB AAAAMAAAAAAAAAAAEAAAMgAAAAEAAAD+////AAAAAC8AAAD///////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// 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//////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////// //////////////////////////////////////8BAP7/AwoAAP////8GCQIA AAAAAMAAAAAAAABGGAAAAE1pY3Jvc29mdCBXb3JkIERvY3VtZW50AAoAAABN U1dvcmREb2MAEAAAAFdvcmQuRG9jdW1lbnQuOAD0ObJxAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA AA== --0-1453715572-1007007347=:20462-- From chemistry-request@server.ccl.net Thu Nov 29 03:10:53 2001 Received: from mail2.zrz.tu-berlin.de ([130.149.4.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAT8ArB05991 for ; Thu, 29 Nov 2001 03:10:53 -0500 Received: from mailszrz.zrz.tu-berlin.de ([130.149.4.11]) by mail2.zrz.tu-berlin.de with esmtp (exim-3.33) id 169MHG-0001PO-00; Thu, 29 Nov 2001 09:10:38 +0100 Received: from natrium.chem.tu-berlin.de ([130.149.169.143]) by mailszrz.zrz.tu-berlin.de with esmtp (exim-3.33) id 169MHG-0006Nr-00; Thu, 29 Nov 2001 09:10:38 +0100 Mime-Version: 1.0 X-Sender: chwu0531@mailszrz.zrz.tu-berlin.de Message-Id: In-Reply-To: <200111281759.fASHxWV69116@mail.rpi.edu> References: <200111281759.fASHxWV69116@mail.rpi.edu> Date: Thu, 29 Nov 2001 09:10:36 +0100 To: "Dr. N. SUKUMAR" From: Christoph van =?iso-8859-1?Q?W=FCllen?= Subject: Re: CCL:collation of responses on ab initio/first principles Cc: chemistry@ccl.net Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id fAT8ArB05992 > >Even the integrals need NOT be evaluated EXACTLY for a method to be called >ab initio. For instance, Gaussian employs several asymptotic and other >cutoffs to approximate integral evaluation. > This is only partly a valid argument. Are sin(x), cos(x), exp(x) etc. calculated "analytically" on any computer? They are computed with similar methods, so erf(x) or F0(x) (or a two-electron integral) is as analytical as any other transcendental function. +---------------------------------+----------------------------------+ | Prof. Christoph van W黮len | Tele-Phone (+49) (0)30 314 27870 | | Technische Universit鋞 Sekr. C3 | Tele-Fax (+49) (0)30 314 23727 | | Stra遝 des 17. Juni 135 | eMail | | D-10623 Berlin, Germany | Christoph.vanWullen@TU-Berlin.De | +---------------------------------+----------------------------------+ -- From chemistry-request@server.ccl.net Thu Nov 29 09:22:34 2001 Received: from ned1.sims.nrc.ca ([132.246.108.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATEMYB11343 for ; Thu, 29 Nov 2001 09:22:34 -0500 Received: from localhost (ps@localhost) by ned1.sims.nrc.ca (8.8.8/8.8.8) with ESMTP id JAA24700; Thu, 29 Nov 2001 09:22:08 -0500 (EST) Date: Thu, 29 Nov 2001 09:22:08 -0500 From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii@nrc.ca To: =?iso-8859-1?Q?Jes=FAs_Rodr=EDguez_Otero?= cc: chemistry@ccl.net Subject: Re: CCL:CADPAC for Linux In-Reply-To: <000c01c17831$fe4d6460$9a4a90c1@usc.es> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=X-UNKNOWN Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id fATEMYB11344 On Wed, 28 Nov 2001, [iso-8859-1] Jes鷖 Rodr韌uez Otero wrote: > Also, I compiled CADPAC with compaq fortran for alpha under Linux, but > when I try to calculate polarisabilituies, the program crashes, with the > following message: [snip] > forrtl: error (65): floating invalid This looks familiar. Try recompiling -everything- (that means literally everything - including all floating-point libraries you link against, including vendor-supplied libraries) using "-mieee" option with GNU compilers, and "-fpe3" option with Compaq compilers (if you use them - which is a good idea in any case). If you are feeling adventurous, you may wish to recompile your cadpac binary with debugging turned on, and track down the offending routine. You can then recompiler just that routine. However, there is no guarantee that the error won't show up in a different place. Unfortunately, this will incur a significant performance loss. If you were running Tru64 Unix, using "-fpe1" option would have had a similar effect, at a lower performance cost. Unfortunately, it is not available under Linux. Regards, Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-991-2719 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii@nrc.ca Research Council Officer Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2158, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From chemistry-request@server.ccl.net Thu Nov 29 09:53:51 2001 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATErpB12033 for ; Thu, 29 Nov 2001 09:53:51 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id JAA24473; Thu, 29 Nov 2001 09:53:44 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3C064429.C77A748F@cornell.edu> Date: Thu, 29 Nov 2001 09:20:26 -0500 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: Re: CCL:charmm parameter References: <200111281722.fASHMkVQ020922@mail.shcnc.AC.CN> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all I apologize for the length of this in advance. But this is info for those that have asked about where to find parameters for CHARMM force fields. It is taken from http://master2.lobos.nih.gov/Charmm/c28a2/parmfile.html. I hope this helps and again I apologize for its length. Richard ======================================================================= File: Parmfile -=- Node: PARMDATA Up: Top -=- Previous: Conversion -=- Next: Top (A) Topology files (1) top_all22_prot.inp all hydrogen RTF for proteins (2) top_all22_model.inp all hydrogen RTF for protein model cmpds (3) top_all22_sugar.rtf all hydrogen RTF for sugars (4) top_all27_na.rtf all hydrogen RTF for nucleic acids (5) top_all27_lipid.rtf all hydrogen RTF for lipids (6) top_all27_na_lipid.rtf all hydrogen RTF for nucleic acids and lipids (7) top_all27_prot_na.rtf all hydrogen RTF for proteins and nucleic acids (9) top_all27_prot_lipid.rtf all hydrogen RTF for proteins and lipids (9) toph19.inp extended atom RTF for proteins (10) toprna10r_22.inp extended atom RTF for nucleic acids (B) Parameter files (1) par_all22_prot.inp all hydrogen parameters for proteins (2) par_all22_sugar.rtf all hydrogen parameters for sugars (3) par_all27_na.rtf all hydrogen parameters for nucleic acids (4) par_all27_lipid.rtf all hydrogen parameters for lipids (5) par_all27_na_lipid.rtf all hydrogen parameters for nucleic acids and lipids (6) par_all27_prot_na.rtf all hydrogen parameters for proteins and nucleic acids (7) par_all27_prot_lipid.rtf all hydrogen parameters for proteins and lipids (8) param19.inp extended atom parameters for proteins (9) pardna10_22.inp extended atom parameters for nucleic acids (10) par_hbond.inp hydrogen bond parameters for analysis only Phased out: The CHARMM22 all-atom nucleic acid and lipid topology and parameter files are no longer included in the toppar directory due to their becoming obsolete. Note that they are included in the toppar_history directories. The CHARMM all-hydrogen topology and parameter sets may be considered to be stable, however, minor bug fixes may be performed as required. Additions may also occur leading to an expanding set of parameters which are compatible across proteins, nucleic acids, lipids, and, ultimately, carbohydrates. The carbohydrate(sugar) parameter work is still in progress by John Brady and coworkers; the number of sugar types should expand in the future. See the file toppar_all.history for a listing changes in the files over time. top_all22_model.inp includes the majority of model compounds used in the protein parameterization and is to be used in conjunction with par_all22_prot.inp. Three sets of combined topology and parameter files are included for use with 1) proteins and nucleic acids, 2) protein and lipids and 3) nucleic acids and lipids. In all cases the CHARMM22 protein parameters and the CHARMM27 nucleic acid or lipid parameters are used. The designation all27 for these files is based on the use of the most recent nucleic acid or lipid parameters. Test calculations using these combined files have yielded good results. Added as of July 1997 was the parameter file par_hbond.inp. This file is included for the analysis of hydrogen bonds; it includes information to calculate h-bond energies, but these are basically meaningless. The hydrogen bonds should NOT be used for energy, minimization and dynamics calculations with the CHARMM all-hydrogen topology and parameter sets. Ions in the all22 files are from two sources. Mg and Ca are from Prodhom and Karplus and were optimized specifically for the all22 parameters. The remaining cations are from Benoit Roux (see his thesis). They were optimized to be consistent with Param19, however, MD studies in a number of groups have shown them to work well. Note the presence of a variety of NBFIXES for the ions. These were initially optimized based on the proteins and later transferred to the lipids and nucleic acids based on analogy (by ADM Jr.). Ions in the all27 files have been optimized based on free energies of solvation by Roux and coworkers. As of August 1999 there were no NBFIXes used with these ions. The extended atom parameters for proteins are the same as those included with CHARMM20 which are based on Wally Reiher's thesis. They have been included in the supplement material of a recent publication (see suggested citations below). For the extended atom nucleic acid parameters those of Nilsson and Karplus, J. Comp. Chem. 7:591-616, 1986 are used which were also included in the CHARMM20 release and are the only set to include explicit hydrogen bonding terms. Some alterations of the extended atom nucleic acid topology and parameter files have been made in order to maintain compatibility with the multiple dihedral scheme in CHARMM22. Please send all remarks and suggestions to alex@mmiris.ab.umd.edu. ADM Jr., August 1999 http://www.pharmacy.ab.umd.edu/~alex/ References PARAM19 PROTEIN PARAMETERS Reiher, III., W.E. Theoretical Studies of Hydrogen Bonding, Ph.D. Thesis, Department of Chemistry, Harvard University, Cambridge, MA, USA, 1985 and Neria, E., Fischer, S., and Karplus, M. Simulation of Activation Free Energies in Molecular Systems, Journal of Chemical Physics, 1996, 105: 1902-21. EXTENDED ATOM NUCLEIC ACID PARAMETERS Nilsson, L. and Karplus,M. Empirical Energy Functions for Energy Minimizations and Dynamics of Nucleic Acids J. Comp. Chem. 7:591-616, 1986 CHARMM22 PROTEIN PARAMETERS MacKerell, J., A.D.; Bashford, D.; Bellott, M.; Dunbrack Jr., R. L.; Evanseck, J.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, I., W. E.; Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-hydrogen Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins using the CHARMM22 Force Field. Journal of Physical Chemistry B, 1998, 102, 3586-3616. FOR PHOSPHOTYROSINE Feng, M.-H., Philippopoulos, M., MacKerell, Jr., A.D., and Lim, C. Structural Characterization of the Phosphotyrosine Binding Region of a High-Affinity SH2 Domain-Phosphopeptide Complex by Molecular Dynamics Simulation and Chemical Shift Calculations, Journal of the American Chemical Society, 1996, 118: 11265-11277 CHARMM27 NUCLEIC ACID PARAMETERS Foloppe, N. and MacKerell, Jr., A.D. "All-Atom Empirical Force Field for Nucleic Acids: 2) Parameter Optimization Based on Small Molecule and Condensed Phase Macromolecular Target Data. Journal of Computational Chemsitry, 2000, 21:86-104. and MacKerell, Jr., A.D. and Banavali, N. "All-Atom Empirical Force Field for Nucleic Acids: 2) Application to Molecular Dynamics Simulations of DNA and RNA in Solution. Journal of Computational Chemsitry, 2000, 21:105-120. CHARMM27 LIPID PARAMETERS Feller, S. and MacKerell, Jr., A.D. manuscript in preparation. NAD+, NADH and PPI Pavelites, J.J., Bash, P.A., Gao, J. and MacKerell, Jr., A.D. A Molecular Mechanics Force Field for NAD+, NADH, and the Pyrophosphate Groups of Nucleotides, Journal of Computational Chemistry, 1997, 18: 221-239. CHARMM22 NUCLEIC ACID PARAMETERS MacKerell Jr., A.D., Wiorkiewicz-Kuczera, J. and Karplus, M. An all-atom empirical energy function for the simulation of nucleic acids, Journal of the American Chemical Society, 1995, 117:11946-11975. CHARMM22 LIPID PARAMETERS Schlenkrich, M., Brickmann, J., MacKerell, Jr., A.D., and Karplus, M. Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications, in "Biological Membranes: A Molecular Perspective from Computation and Experiment," K.M. Merz and B. Roux, Eds. Birkhauser, Boston, 1996, pp 31-81. FOR ALKENES Feller, S.E., Yin, D., Pastor, R.W., and MacKerell, Jr., A.D., Molecular Dynamics Simulation of Unsaturated Lipids at Low Hydration: Parametrization and Comparison with Diffraction Studies. Biophysical Journal 1997, 73: 2269-2279. ======================================================================== -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Thu Nov 29 10:25:35 2001 Received: from post.tau.ac.il ([132.66.16.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATFPYB12709 for ; Thu, 29 Nov 2001 10:25:34 -0500 Received: from post.tau.ac.il (pico.tau.ac.il [132.66.145.20]) by post.tau.ac.il (8.11.6/8.11.6) with ESMTP id fATFPRP26131 for ; Thu, 29 Nov 2001 17:25:27 +0200 (IST) Sender: silviu@post.tau.ac.il Message-ID: <3C065366.E57F6BE0@post.tau.ac.il> Date: Thu, 29 Nov 2001 15:25:26 +0000 From: Zilberman Silviu Organization: TAU X-Mailer: Mozilla 4.7 [en] (X11; I; Linux 2.2.10 i686) X-Accept-Language: en MIME-Version: 1.0 To: ccl Subject: automatic parallelization Content-Type: multipart/mixed; boundary="------------8268FB352AB4B49DAC34ED05" This is a multi-part message in MIME format. --------------8268FB352AB4B49DAC34ED05 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi everyone, Does anyone has experience with using auotmatic parallelization tools, for old Fortran and C codes? We are buying a PC cluster, and I look for a quick and dirty way of getting parallel codes out of seriel one. Thanks, Silviu Zilberman. -- %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Zilberman Silviu School of Chemistry, Tel Aviv University Ramat Aviv, Tel-Aviv, Israel 61391 Phones 972-3-6407634 (office) 972-3-6409293 (fax 1 - School of Chemistry) 972-3-6423765 (fax 2 - Prof. A. Nitzan) mailto:silviu@post.tau.ac.il Home Page: http://femto.tau.ac.il/~silviu %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% --------------8268FB352AB4B49DAC34ED05 Content-Type: text/x-vcard; charset=us-ascii; name="silviu.vcf" Content-Transfer-Encoding: 7bit Content-Description: Card for Zilberman Silviu Content-Disposition: attachment; filename="silviu.vcf" begin:vcard n:Zilberman;Silviu tel;work:972-3-6407634 x-mozilla-html:TRUE org:Tel Aviv University;School of Chemistry version:2.1 email;internet:silviu@post.tau.ac.il adr;quoted-printable:;;Tel Aviv University=0D=0ASchool of Chemistry;Tel Aviv;;69978;Israel x-mozilla-cpt:;-17216 fn:Silviu Zilberman end:vcard --------------8268FB352AB4B49DAC34ED05-- From chemistry-request@server.ccl.net Thu Nov 29 10:46:15 2001 Received: from guppy.vub.ac.be ([134.184.129.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATFkEB13245 for ; Thu, 29 Nov 2001 10:46:15 -0500 Received: from mach.vub.ac.be (mach.vub.ac.be [134.184.129.3]) by guppy.vub.ac.be (8.9.1b+Sun/3.17.1.ap (guppy)) id QAA22766; Thu, 29 Nov 2001 16:46:03 +0100 (MET) for Received: from vub.ac.be (algcpc5.vub.ac.be [134.184.24.95]) by mach.vub.ac.be (8.9.3/3.13.3.ap (mach)) id QAA12716; Thu, 29 Nov 2001 16:46:05 +0100 (MET) for Message-ID: <3C065840.1010009@vub.ac.be> Date: Thu, 29 Nov 2001 16:46:08 +0100 From: Pierre Mignon User-Agent: Mozilla/5.0 (Windows; U; Win98; en-US; rv:0.9.4) Gecko/20011019 Netscape6/6.2 X-Accept-Language: en-us MIME-Version: 1.0 To: chemistry@ccl.net Subject: amber parameters Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Hello, I want to use the Amber force field, but I have a problem to parametrise the calcium atom. Does anyone know where could I find such parameters ? Thank's in advance . Pierre Mignon PhD student. From chemistry-request@server.ccl.net Thu Nov 29 11:06:56 2001 Received: from mailbox.engr.sc.edu ([129.252.21.5]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATG6uB13645 for ; Thu, 29 Nov 2001 11:06:56 -0500 Received: from samay (samay.ee.sc.edu [129.252.22.248]) by mailbox.engr.sc.edu with SMTP (Microsoft Exchange Internet Mail Service Version 5.5.2653.13) id X20HJYVZ; Thu, 29 Nov 2001 11:05:51 -0500 Message-ID: <008e01c178ef$ca7d2300$f816fc81@ee.sc.edu> From: "derosa" To: Subject: Fw: CCL:automatic parallelization Date: Thu, 29 Nov 2001 11:06:23 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 I will be interested on a summary of responses to this question. I would also like to make the question extensive to quick ways of parallelization on workstations. Thanks, Pedro ----- Original Message ----- From: "Zilberman Silviu" To: "ccl" Sent: Thursday, November 29, 2001 10:25 AM Subject: CCL:automatic parallelization > Hi everyone, > > Does anyone has experience with using auotmatic parallelization tools, > for old Fortran and C codes? > We are buying a PC cluster, and I look for a quick and dirty way of > getting parallel codes out of seriel one. > > Thanks, > Silviu Zilberman. > > -- > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > Zilberman Silviu > > School of Chemistry, Tel Aviv University > Ramat Aviv, Tel-Aviv, Israel 61391 > > Phones > 972-3-6407634 (office) > 972-3-6409293 (fax 1 - School of Chemistry) > 972-3-6423765 (fax 2 - Prof. A. Nitzan) > > mailto:silviu@post.tau.ac.il > Home Page: http://femto.tau.ac.il/~silviu > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > > From chemistry-request@server.ccl.net Thu Nov 29 10:51:49 2001 Received: from mail.chem.tamu.edu (IDENT:root@[165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATFpmB13330 for ; Thu, 29 Nov 2001 10:51:49 -0500 Received: from [165.91.177.32] (account yubofan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5b3) with ESMTP id 734148 for CHEMISTRY@ccl.net; Thu, 29 Nov 2001 09:45:28 -0600 Sender: yubo@ccl.net Message-ID: <3C06598B.58059D17@mail.chem.tamu.edu> Date: Thu, 29 Nov 2001 09:51:39 -0600 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: en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: Summary:GIF file with frequency animation Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id fATFpnB13331 Hi, This is the summary for creating animated gif or mpeg files of vibrations of molecules from G98's output. Hi, Guassview and HyperChem can visualize vibrational modes calculated by G98, to my knowledge. But, they can't export the animations to any format that common programs, such as Windows MediaPlayer, can load. In fact, I want to create some animated GIF files for some frequencies. I mean if I can capture 4 or 5 pictures from Guassview or HyperChem's animation, these GIF files can be created correctly. Any advice? Thanks in advance Yubo ================================================ gOpenMol (available free from Leif Laaksonen) can do this - it will write MPEGs. You can also get it to write out a set of bitmap files for each frame of your trajectory and then use some program like Paintshop Pro (for windows) to make animated GIFs. See the gOpenMol link on my web page for a tutorial on gOpenMol that includes instructions on downloading. Prof. Scott L. Anderson Department of Chemistry University of Utah 315 S. 1400 E. Rm 1216 Salt Lake City, UT 84112 (801)585-7289 FAX(801)581-8433 www.chem.utah.edu/chemistry/faculty/anderson/anderson.html ================================================ GIMP (http://www.gimp.org/) will create animated gif files for you (and much, much more). GIMP is free, and is available for both windows, and unix platforms. Dr. Serguei Patchkovskii Tel: +1-(613)-991-2719 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii@nrc.ca Research Council Officer Steacie Institute for Molecular Sciences National Research Council Canada Room 2158, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada ================================================ I have done this sort of thing with molekel and paintshop pro. molekel can save an image as a .gif file; paintshop can string these together to make and nimated .gif file. I have attached an example of this: an animation that shows the decomposition of carbonic acid. This is the result of an IRC calculation in gaussian. Steve Steve Williams A. R. Smith Department of Chemistry Appalachian State University Boone, NC 28608 USA 828-262-2965 ================================================ I looked at that too. I did not find an easy solution. What I do is install X-win (eg from www.starnet.com-you: they give a trial version and then you have to buy a license, but I heard there might be a crack), then install molden (http://www.caos.kun.nl/~schaft/molden/molden.html) on my windows-pc and show the vibration. A second option is to let molden make a gif file > from every screen update while you visualise a vibration. All these files can then be grouped into a .mov file (I use a program that comes with coreldraw). A third option is to use a screen grabbing utility. I know my collegue uses this on a silicon graphics O2-I don't know if it available for your installation. I hope this help. If you come up with a better solution I would be interested to hear about it! Best Regards, Mark Saeys Laboratory for Petrochemical Engineering Ghent University Krijgslaan 281 (S5) B9000 Gent Belgium tel: .32.(0)9.264.56.78 fax: .32.(0)9.264.49.99 http://lptnt01.rug.ac.be/chemical.engineering ================================================ I don't use Windows much at all, but I'd expect there are any number of screen-capture or screenshot programs available. Couldn't you use these to take a shot of each frame and then import them into a program for a GIF animation? Certainly not as nice as being able to save frames e.g.: molecule-frame1.gif molecule-frame2.gif ... I certainly know Linux and MacOS have programs that will capture the graphics in a particular window, so Windows should also have them. -- -- -Geoff Hutchison Ratner/Marks Groups (847) 491-3295 Northwestern Chemistry http://www.chem.nwu.edu/ ================================================ perhaps one idea. Molden is able to write a gif per screen update. So you can animate and write gifs at the same time. With common grafic programs it should be able to merge the single files to an animated gif. Perhaps there is a similar way in gv and Hyperchem .... Hope this helps Alex --- Dr. Alexander Hofmann Institute for Applied Chemistry Berlin-Adlershof P.O. Box 96 11 56 Richard-Willstaetter-Str. 12 D-12474 Berlin D-12489 Berlin hofmann@aca-berlin.de Tel.: +49-30-6392-4408 Fax.: +49-30-6392-4350 http://www.aca-berlin.de ================================================ An example of an animated gif-file created this way can be seen on this web-page: http://Virgil.ruc.dk/kurser/KemFys2/adm_opg.htm It shows the "bell-clapper" vibration of trithiapentalene, and was created by Jens Peter Jensen and Morten Langgaard by capturing images > from HyperChem's vibrational mode animation. Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- JENS SPANGET-LARSEN Office: +45 4674 2710 Department of Chemistry Fax: +45 4674 3011 Roskilde University (RUC) Cell-Phone: +45 2320 6246 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://virgil.ruc.dk/~jsl =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=- ================================================ molden and gifmoviegear http://www.caos.kun.nl/~schaft/molden/molden.html http://www.gamani.com/ -Phil Matz ================================================ Hi Yubo, There is some soft - known as video grabbers - which is capabele to take the snapshots from your monitor, while vibratin animations play. Better way - in my mind - use gOpenmol. There is option to export normal modes vibrations into MPEG, via making TGA files. Later you can convert TGA to GIF files for each frame. Then you can bring all frames together in any GIF animation sotware (there is sharaware as well). That's all. Good luck - I think it'll help you :-) Arturas ================================================ From chemistry-request@server.ccl.net Thu Nov 29 12:01:02 2001 Received: from gatekeeper2.novartis.com ([194.191.169.74]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATH11B15096 for ; Thu, 29 Nov 2001 12:01:01 -0500 Received: from mtap1.is.chbs (mtap1.novartis.com [192.37.33.20]) by gatekeeper2.novartis.com (8.11.0/8.11.0) with ESMTP id fATH0qO29719 for ; Thu, 29 Nov 2001 18:00:52 +0100 (MET) Received: from NVCHBS-S0121.is.chbs (nvchbs-s0121.is.chbs [192.37.33.41]) by mtap1.is.chbs (8.11.3/8.11.3) with ESMTP id fATH0pT268914 for ; Thu, 29 Nov 2001 18:00:51 +0100 Subject: mol-3D-2D To: chemistry@ccl.net From: maria.brandl@pharma.novartis.com Date: Thu, 29 Nov 2001 18:00:13 +0100 Message-ID: X-MIMETrack: Serialize by Router on CHBSMN12/N1/Novartis(Release 5.0.8 |June 18, 2001) at 11/29/2001 06:00:51 PM MIME-Version: 1.0 Content-type: text/plain; charset=us-ascii Hi CCL-ers, Does anybody know/currently write/ need a tool that converts mol-files with 3D - coordinates into mol-files with 2D - coordinates and correct stereo- chemisty, up/down bonds etc.. and the same atom numbering as the original file. A tool that could reassign original atom numbering of the 3D-file a correct 2D-file with changed order of atoms would do as well. Greetings, Maria From chemistry-request@server.ccl.net Thu Nov 29 12:37:01 2001 Received: from web12101.mail.yahoo.com ([216.136.172.21]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fATHb1N16736 for ; Thu, 29 Nov 2001 12:37:01 -0500 Message-ID: <20011129173655.91044.qmail@web12101.mail.yahoo.com> Received: from [160.114.63.170] by web12101.mail.yahoo.com via HTTP; Thu, 29 Nov 2001 17:36:55 GMT Date: Thu, 29 Nov 2001 17:36:55 +0000 (GMT) From: =?iso-8859-1?q?Denys=20Bashtovyy?= Subject: DMPG structure in PDB format To: chemistry@server.ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear All, Could anybody point me to the freely available DMPG structure in PDB format? I a m aware of one at http://www.biochem.missouri.edu/~lesa/LIPIDS/LIPIDS/di.html#DM PG but, unfortunately, it lacks glycerol headgroup (which should be available in 2 mirror conformations). Thanks in advance, Denys __________________________________________________ Do You Yahoo!? Everything you'll ever need on one web page from News and Sport to Email and Music Charts http://uk.my.yahoo.com From chemistry-request@server.ccl.net Thu Nov 29 11:09:10 2001 Received: from garaged.fis.unam.mx ([132.248.33.226]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATG99B13724 for ; Thu, 29 Nov 2001 11:09:09 -0500 Received: from yahoo.com (localhost [127.0.0.1]) by garaged.fis.unam.mx (8.11.6/8.11.6) with ESMTP id fAT49gJ06730 for ; Wed, 28 Nov 2001 22:09:42 -0600 Sender: max@garaged.fis.unam.mx Message-ID: <3C05B505.A302DAC2@yahoo.com> Date: Wed, 28 Nov 2001 22:09:42 -0600 From: Max Valdez X-Mailer: Mozilla 4.78 [es] (X11; U; Linux 2.4.9-ac18 i686) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Re: CCL:Spartan vs Gaussian (try NWCHEM for FREE!) References: <5FBD82D1CB46D511AAEA0002A55C6F5202AAA968@rbamsem3.bas.roche.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit NWChem its free, for almos ANY plataform, and comes with parallel porting, pretty easy to implement http://www.emsl.pnl.gov:2080/docs/nwchem/nwchem.html Regards Max From chemistry-request@server.ccl.net Thu Nov 29 12:34:48 2001 Received: from phobos.email.Arizona.EDU (IDENT:root@[128.196.133.165]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATHYmN16675 for ; Thu, 29 Nov 2001 12:34:48 -0500 Received: from u.arizona.edu (128.196.184.158) by phobos.email.Arizona.EDU (6.0.034) (authenticated as mcafiero@email.arizona.edu) id 3C052983000220D1; Thu, 29 Nov 2001 10:34:38 -0700 Sender: mcafiero@ccl.net Message-ID: <3C0671AF.6C057D17@u.arizona.edu> Date: Thu, 29 Nov 2001 17:34:39 +0000 From: Maurice Cafiero X-Mailer: Mozilla 4.61 [en] (X11; I; Linux 2.2.13-7mdk i686) X-Accept-Language: en MIME-Version: 1.0 To: Zilberman Silviu CC: ccl Subject: Re: CCL:automatic parallelization References: <3C065366.E57F6BE0@post.tau.ac.il> Content-Type: multipart/alternative; boundary="------------DF0584890DDE7E7B034B0A4F" --------------DF0584890DDE7E7B034B0A4F Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit hello: I have used the automatic parallelization tools that come with SGI Fortan, and they are pretty terrible. They created a 2/3% speedup and were about 5% parallel. I suggest 2 things: 1) Use parallel numerical libraries. These are pre-existing and can probably be downloaded from netlib. 2) Learning basic MPI is not difficult at all for an experienced FORTRAN programmer. I learned it in about 3 weeks and my code is 80/90% parallel. I get excellent speedup (approximately linear with # procs). What type of program are you trying to parallelize? -- Mauricio Cafiero Doctoral Candidate : Theoretical and Computational Quantum Chemistry Department of Chemistry University of Arizona --------------DF0584890DDE7E7B034B0A4F Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit hello:
    I have used the automatic parallelization tools that come with SGI Fortan, and they
are pretty terrible. They created a 2/3% speedup and were about 5% parallel.
    I suggest 2 things:

    1) Use parallel numerical libraries. These are pre-existing and can probably be downloaded
          from netlib.

    2) Learning basic MPI is not difficult at all for an experienced FORTRAN programmer.
          I learned it in about 3 weeks and my code is 80/90% parallel. I get excellent speedup
          (approximately linear with # procs).

What type of program are you trying to parallelize? 

-- 
Mauricio Cafiero
Doctoral Candidate : Theoretical
                     and Computational
                     Quantum Chemistry
Department of Chemistry
University of Arizona
  --------------DF0584890DDE7E7B034B0A4F-- From chemistry-request@server.ccl.net Thu Nov 29 11:45:08 2001 Received: from ribotargets.com ([194.129.39.11]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATGj8B14686 for ; Thu, 29 Nov 2001 11:45:08 -0500 Received: from szilva (helo=localhost) by echo.ribotargets.com with local-esmtp (Exim 3.13 #1) id 169UGO-0001Gj-00; Thu, 29 Nov 2001 16:42:16 +0000 Date: Thu, 29 Nov 2001 16:42:16 +0000 (GMT) From: Szilveszter Juhos To: Ng Pei Ling cc: chemistry@ccl.net Subject: Re: CCL:HETATM In-Reply-To: <20011129041547.20667.qmail@web14914.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Wed, 28 Nov 2001, Ng Pei Ling wrote: > find HETATM in my Protein Data Bank file. But, I don't know what is > the meaning of HETATM file. May I know the answer of below question ? http://pdb.ccdc.cam.ac.uk/pdb/docs/format/pdbguide2.2/guide2.2_frame.html Szilva From chemistry-request@server.ccl.net Thu Nov 29 16:21:05 2001 Received: from bute.st-andrews.ac.uk (im17@[138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATLL5N21157 for ; Thu, 29 Nov 2001 16:21:05 -0500 Received: from localhost (im17@localhost) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with SMTP id VAA15332; Thu, 29 Nov 2001 21:13:35 GMT Date: Thu, 29 Nov 2001 21:13:35 +0000 (GMT) From: Ibrahim Moustafa X-Sender: im17@st-andrews.ac.uk To: Ng Pei Ling cc: chemistry@ccl.net Subject: Re: CCL:HETATM In-Reply-To: <20011129041547.20667.qmail@web14914.mail.yahoo.com> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Ng, The HETATM records present the atomic coordinate records for atoms within "non-standard" groups. These records are used for water molecules and atoms presented in HET groups. HET records are used to describe non-standard residues, such asprosthetic groups, inhibitors, solvent molecules,and ions for which coordinates are supplied. Groups are considered HET if they are: - not one of the standard amino acids, and - not one of the nucleic acids (C, G, A, T, U, and I), and - not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and - not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name. You can find more information about the PDB format in the site: http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html Cheers, Ibrahim Name :Ibrahim M.Moustafa Mail address:Center for Biomolecular Science, BIOMOLECULAR SCIENCE BUILDING, North Haugh,St-Andrews, Fife,KY16 9ST Scotland,U.K. Tel :+44(0)1334-467257 E-mail :im17@st-andrews.ac.uk On Wed, 28 Nov 2001, Ng Pei Ling wrote: [NON-Text Body part not included] From chemistry-request@server.ccl.net Thu Nov 29 15:56:59 2001 Received: from web13403.mail.yahoo.com ([216.136.175.61]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fATKuxN20718 for ; Thu, 29 Nov 2001 15:56:59 -0500 Message-ID: <20011129205653.48589.qmail@web13403.mail.yahoo.com> Received: from [169.232.140.206] by web13403.mail.yahoo.com via HTTP; Thu, 29 Nov 2001 12:56:53 PST Date: Thu, 29 Nov 2001 12:56:53 -0800 (PST) From: eric hu Subject: SUMMARY: flat potential surface To: chemistry@ccl.net Cc: hxt10@po.cwru.edu MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, All A couple weeks ago I asked the following question: Dear ALL, If the potential surface happens to be flat at the transition state region, what is the best way to find the 1st transition state. I tried to use conventional optimization method in G98 and it always produced an imaginary frequency which is not along the reaction coordinate. I had a few kind responses and tried some of the suggestions. Unfortunately neither of them is working so far. Maybe it's because dft cannot handle the diradical species very well as seen in other examples. Here is the summary I got from some folks. Thanks again for all your suggestions! Suggestions: 1) use qst2 or qst3 2) use opt=calcfc 3) use scf=tight, opt=(calcfc,tight) 4) use int=(grid=ultrafine) scf=novaracc if using dft 5) scan the co-ordinate and use two points on either size of the maximum as the starting poitn for qst2/qst3 6) if calcuating a loose complex or A+B->C then order the atoms carefully to keep more tightly bonded atoms on both sides next to one another 7) go back to opt=(ts,calcfc) if qst2/qst3 completely fail near the ts. ... if after this, the surface is very flat, and the numerical surface differs from the analytical surface, it may be practically impossible to find a well-converged 1st order transition state using g98. If you find a way to handle this case, I'd like to hear about it. hope this helps a little, Jeremy ---------------------------------------------------------------------- Jeremy Greenwood jeremy.greenwood@i.am Department of Medicinal Chemistry bh +45 35306117 Royal Danish School of Pharmacy fx +45 35306040 Universitetsparken 2, DK-2100 Copenhagen, Denmark ah +45 32598030 ---------------------------------------------------------------------- On the other hand, the early worm gets eaten. Men det kaern der kommer foerst til moellen, bliver foerst malet. ---------------------------------------------------------------------- Dear Eric, Which method are you using:DFT or HF/post-HF? If you are using DFT I am afraid it might not be so happy with the diradicals. Secondly, if it is a radical reaction, I am really suspicious of the presence of a pre- or post- reaction complex... Also with QST2 and QST3 one should be very careful while matching the atoms. Have you tried the options noeigen and nrscale whith opt? opt=(ts,noeigen,nrscale,calcfc) is my favorite for TS calculations. Sometimes Basis set superposition error can give lower TS than they actually are. There is a keyword 'massage' for that but I think this is an extreme case. You can lower the convergence threshold but that will cost you some loss in accuracy. Or maybe you can optimize the geometry with lower convergence and then take this output and use it as an input for further optimization with higher convergence. You can also 'freeze' the reaction coordinate and optimize the rest of the molecule. Then you can 'relax'the reaction coordinate too for further calculations... I hope you get the TS you are looking for soon.. Sincerely yours Alimet Ozen ozensem@boun.edu.tr Dear Eric, First of all it depends on your reaction I think. There might be a complex located below GS and TS structures on PES. Also how about tunnelling, if there is a proton transfer, for example, in your reaction? You might try Opt=QST2 option in Gaussian, once it gave me very good results. Also you can optimize the TS first using a semi-empirical method in Spartan or Mopac or anything and then use the output geometry as an input in gaussian calculation. Sincerely yours Alimet Ozen ozensem@boun.edu.tr __________________________________________________ Do You Yahoo!? Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From chemistry-request@server.ccl.net Thu Nov 29 16:03:32 2001 Received: from web13401.mail.yahoo.com ([216.136.175.59]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fATL3WN20853 for ; Thu, 29 Nov 2001 16:03:32 -0500 Message-ID: <20011129210325.35592.qmail@web13401.mail.yahoo.com> Received: from [169.232.140.206] by web13401.mail.yahoo.com via HTTP; Thu, 29 Nov 2001 13:03:25 PST Date: Thu, 29 Nov 2001 13:03:25 -0800 (PST) From: eric hu Subject: binding energy contributions from vdw and coul To: chemistry@ccl.net MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Hi, all I'm working on binding energy calculation of an antibody with its hapten. So far I've been using AMBER and LIAISON (from Schrodinger company) to calculate the linear response energy (LIE). I'm very interested calculating the individual binding energy contributions from vdw and coul interactions. I was wondering if ther are other methods that can do this job. Thanks. Eric __________________________________________________ Do You Yahoo!? Yahoo! GeoCities - quick and easy web site hosting, just $8.95/month. http://geocities.yahoo.com/ps/info1 From chemistry-request@server.ccl.net Thu Nov 29 16:34:47 2001 Received: from hotmail.com ([64.4.8.147]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATLYlN21596 for ; Thu, 29 Nov 2001 16:34:47 -0500 Received: from mail pickup service by hotmail.com with Microsoft SMTPSVC; Thu, 29 Nov 2001 13:34:36 -0800 Received: from 130.108.137.142 by lw9fd.law9.hotmail.msn.com with HTTP; Thu, 29 Nov 2001 21:34:36 GMT X-Originating-IP: [130.108.137.142] From: "Casey Kelly" To: chemistry@ccl.net Subject: ZINDO/SCRF method Date: Thu, 29 Nov 2001 15:34:36 -0600 Mime-Version: 1.0 Content-Type: text/html Message-ID: X-OriginalArrivalTime: 29 Nov 2001 21:34:36.0896 (UTC) FILETIME=[A4CC7600:01C1791D]
Is anyone familiar with a software program (Windows) that is capable of performing ZINDO (INDO/s) calculations in the presence of a solvent?  I would like to determine solvatochromic shifts for a series of dyes using the ZINDO method in accordance with an SCRF.  Any suggestions would be greatly appreciated and all useful replies will be summarized and submitted to the list.   

 
Casey Kelly
Wright State University
 

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From chemistry-request@server.ccl.net Thu Nov 29 17:02:59 2001 Received: from gordon.chem.wayne.edu (mer@[141.217.26.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATM2xN22207 for ; Thu, 29 Nov 2001 17:02:59 -0500 Received: from localhost (mer@localhost) by gordon.chem.wayne.edu (8.10.2+Sun/8.10.2) with ESMTP id fATM2o018698 for ; Thu, 29 Nov 2001 17:02:50 -0500 (EST) Date: Thu, 29 Nov 2001 17:02:50 -0500 (EST) From: "mer@chem.wayne.edu" To: chemistry@server.ccl.net Subject: dynamical cross-correlation matrices Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear All, I am wondering if anyone knows of any software (preferably free) that would compute dynamical cross-crrelation matrices for a protein simulation. What other software could be used to display it in color coded 2D plot? I have a trajectory in AMBER coordinate file format. Thanks. From chemistry-request@server.ccl.net Thu Nov 29 18:25:36 2001 Received: from bute.st-andrews.ac.uk (im17@[138.251.12.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fATNPZN25222 for ; Thu, 29 Nov 2001 18:25:35 -0500 Received: from localhost (im17@localhost) by bute.st-andrews.ac.uk (8.9.1a/8.9.1) with SMTP id XAA18848; Thu, 29 Nov 2001 23:25:11 GMT Date: Thu, 29 Nov 2001 23:25:11 +0000 (GMT) From: Ibrahim Moustafa X-Sender: im17@st-andrews.ac.uk To: "mer@chem.wayne.edu" cc: chemistry@server.ccl.net Subject: Re: CCL:dynamical cross-correlation matrices In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII I'm interested in your question, can you pass the answers to me. many thanks, Ibrahim Name :Ibrahim M.Moustafa Mail address :Center for Biomolecular Science, BIOMOLECULAR SCIENCE BUILDING, North Haugh,St-Andrews, Fife,KY16 9ST Scotland,U.K. Tel :+44(0)1334-467257 E-mail :im17@st-andrews.ac.uk On Thu, 29 Nov 2001, mer@chem.wayne.edu wrote: > Dear All, > I am wondering if anyone knows of any software (preferably free) > that would compute dynamical cross-crrelation matrices for a protein > simulation. What other software could be used to display it in color > coded 2D plot? I have a trajectory in AMBER coordinate file format. > Thanks. > > > -= 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 Thu Nov 29 19:45:11 2001 Received: from iris.sipp.ac.cn ([202.127.25.14]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAU0j9N28352 for ; Thu, 29 Nov 2001 19:45:10 -0500 Received: from iris.sipp.ac.cn [202.127.18.184] by iris.sipp.ac.cn with ESMTP (SMTPD32-6.04) id A9434B18010C; Fri, 30 Nov 2001 08:56:35 +0800 Sender: swift@ccl.net Message-ID: <3C06D9BD.26D5838F@iris.sipp.ac.cn> Date: Fri, 30 Nov 2001 08:58:37 +0800 From: Mao Xiang Organization: iris.sipp.ac.cn 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: optimization energy as a index of stability Content-Type: text/plain; charset=gb2312 Content-Transfer-Encoding: 7bit Hello: everyone: I wonder if the stability of a mutant could be compared with the wild type, just compare the minimization energy difference in the same modeling package, such as in insightII. Thanks. Regards, mao xiang From chemistry-request@server.ccl.net Thu Nov 29 21:30:50 2001 Received: from femail1.sdc1.sfba.home.com ([24.0.95.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAU2UoN32404 for ; Thu, 29 Nov 2001 21:30:50 -0500 Received: from C1353359A ([65.4.172.51]) by femail1.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011130023043.WRWY13622.femail1.sdc1.sfba.home.com@C1353359A>; Thu, 29 Nov 2001 18:30:43 -0800 Message-ID: <005d01c17946$55251610$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: "Casey Kelly" , References: Subject: Re: CCL:ZINDO/SCRF method Date: Thu, 29 Nov 2001 18:25:52 -0800 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_005A_01C17903.46CAE790" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 This is a multi-part message in MIME format. ------=_NextPart_000_005A_01C17903.46CAE790 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable ArgusLab is perfect for calculations on dye molecules using ZINDO and = SCRF. It runs on Windows, performs Zindo calculations and has a very nice = interface to Zerner's SCRF method with automatic calculation of solute = cavity radius and a series of common solvents to choose from (or you can = type in your own solvent parameters). Furthermore, it has a great molecule builder and surface rendering = capability. You can make terrific surfaces showing, for example, the enhancement of = the shift in electron density, electrostatic potential, etc, from the = ground to excited states comparing SCRF calculations with gas-phase = calculations. I've put some sample surfaces on the website at the Planaria image = gallery (http://www.planaria-software.com/gallery.htm) You can obtain version 2.0 and version 3.0 beta from = http://www.planaria-software.com Enjoy, Mark To: chemistry@ccl.net=20 Sent: Thursday, November 29, 2001 1:34 PM Subject: CCL:ZINDO/SCRF method=20 Is anyone familiar with a software program (Windows) that is capable = of performing ZINDO (INDO/s) calculations in the presence of a solvent? = I would like to determine solvatochromic shifts for a series of dyes = using the ZINDO method in accordance with an SCRF. Any suggestions = would be greatly appreciated and all useful replies will be summarized = and submitted to the list. =20 =20 Casey Kelly Wright State University caseykelly70@hotmail.com ------=_NextPart_000_005A_01C17903.46CAE790 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
ArgusLab is perfect for = calculations=20 on dye molecules using ZINDO and SCRF.
 
It runs on Windows, performs Zindo=20 calculations and has a very nice interface to Zerner's SCRF method with=20 automatic calculation of solute cavity radius and a series of common = solvents to=20 choose from (or you can type in your own solvent = parameters).
 
Furthermore, it has a great molecule = builder=20 and surface rendering capability.
 
You can make terrific surfaces = showing, for=20 example, the enhancement of the shift in electron density, = electrostatic=20 potential, etc,  from the ground to excited states comparing = SCRF=20 calculations with gas-phase calculations.
 
I've put some sample surfaces on the = website=20 at the Planaria image gallery (http://www.planaria= -software.com/gallery.htm)
 
You can obtain version 2.0 and = version 3.0=20 beta from http://www.planaria-software.co= m
 
Enjoy,
Mark
 
Sent: Thursday, November 29, = 2001 1:34=20 PM
Subject: CCL:ZINDO/SCRF method =

Is anyone familiar with a software program = (Windows) that is=20 capable of performing ZINDO (INDO/s) calculations in the presence of a = solvent?  I would like to determine solvatochromic shifts for a = series of=20 dyes using the ZINDO method in accordance with an SCRF.  Any = suggestions=20 would be greatly appreciated and all useful replies will be summarized = and=20 submitted to the list.   

 
Casey Kelly
Wright State University
caseykelly70@hotmail.com
 
 
------=_NextPart_000_005A_01C17903.46CAE790-- From chemistry-request@server.ccl.net Thu Nov 29 17:19:46 2001 Received: from mail.axelero.hu ([195.228.240.83]) by server.ccl.net (8.11.6/8.11.0) with SMTP id fATMJjN22548 for ; Thu, 29 Nov 2001 17:19:45 -0500 Received: (qmail 13663 invoked from network); 29 Nov 2001 22:18:46 +0100 Received: from adsl95.225.axelero.hu (HELO chemaxon.com) (195.228.225.95) by mail.axelero.hu with SMTP; 29 Nov 2001 22:18:46 +0100 Message-ID: <3C06A5C2.5060209@chemaxon.com> Date: Thu, 29 Nov 2001 22:16:50 +0100 From: Ferenc Csizmadia Organization: ChemAxon User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:0.9.2) Gecko/20010726 Netscape6/6.1 X-Accept-Language: en-us, hu MIME-Version: 1.0 To: maria.brandl@pharma.novartis.com, chemistry@ccl.net Subject: Re: CCL:mol-3D-2D References: Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit Maria, >Does anybody know/currently write/ >need a tool that converts mol-files with 3D - coordinates >into mol-files with 2D - coordinates and correct stereo- >chemisty, up/down bonds etc.. and the same atom numbering >as the original file. > A tool that could reassign original atom numbering >of the 3D-file a correct 2D-file with changed order of atoms >would do as well. > There is a command-line tool that can do that in the Marvin Beans package of ChemAxon. The tool is called MolConverter. It interconverts various file formats (Molfile, SDF, SMILES, ....) and also creates image files. I guess you need Molfile to Molfile or SDfile to SDfile conversion. (The same atom numbering is applied in the generated 2D-file as in the original 3D file) If you would like to try MolConverter, select "Marvin" at http://www.chemaxon.com/products.html and then choose "Download". On the download page select "Downloads for web and software developers. (Applets and JavaBeans) ". (I guess, you are not a software developer, but usually developers are interested in Marvin Beans) Since Molconverter is in Java, you need to install a Java Runtime Environment before running it. The page explains how to register before downloading and how to get Java. When you are done, select the marvinbeans-.....zip link. Unzip the file, go to the marvinbeans directory (in a Command Prompt or a Unix shell window) and run bin_MSWIN\molconvert mol -2:O1 filename (in Windows) bin/molconvert mol -2:O1 filename (in Unix) (if you need a format other than Molfile, then replace "mol" with the abbreviation of another format) A user guide for Molconverter is available at http://www.chemaxon.com/marvin/doc/molconvert.html. Another product called JChem (it is for chemical database handing) also includes the MolConverter. But probably you are better off with Marvin Beans, since it is smaller. Please let me me know if you need help. Best regards, Ferenc -- Dr. Ferenc Csizmadia ChemAxon Ltd. http://www.chemaxon.com T:+3620 9570988 From chemistry-request@server.ccl.net Thu Nov 29 21:25:03 2001 Received: from femail20.sdc1.sfba.home.com ([24.0.95.129]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fAU2P3N32089 for ; Thu, 29 Nov 2001 21:25:03 -0500 Received: from C1353359A ([65.4.172.51]) by femail20.sdc1.sfba.home.com (InterMail vM.4.01.03.20 201-229-121-120-20010223) with SMTP id <20011130022452.WIBV23568.femail20.sdc1.sfba.home.com@C1353359A>; Thu, 29 Nov 2001 18:24:52 -0800 Message-ID: <005301c17945$83ba3f10$33ac0441@sttln1.wa.home.com> Reply-To: "Mark A. Thompson" From: "Mark A. Thompson" To: "Borosy, Andras {Basi~Basel}" , References: <5FBD82D1CB46D511AAEA0002A55C6F5202AAA968@rbamsem3.bas.roche.com> Subject: Re: CCL:Spartan vs Gaussian Date: Thu, 29 Nov 2001 18:20:00 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 If you have virtually no money, try ArgusLab. Granted it does not do ab initio calculations, but it does have all the usual semi-empirical methods, and UFF for the entire periodic table, and very nice graphics and surface rendering capabilities competetive with the expensive professional packages. Also, you can render surfaces from calculations done with Gaussian if you choose not to use GaussView. http://www.planaria-software.com Mark ----- Original Message ----- From: "Borosy, Andras {Basi~Basel}" To: Sent: Wednesday, November 28, 2001 9:52 AM Subject: CCL:Spartan vs Gaussian > Deat Colleague, > > Spartan has been dedicated for computational medicinal and organic chemsitry. It is cheaper then Gaussian, but much more userfriend and has a decent graphics. If you need model d and f field compounds and/or you have more money, buy Gaussian! If you have much more money, buy Jaguar! > > Best wishes, > > Andr醩 Borosy > > Basilea Pharmaceutica Ltd > POB 3255, 65/316B > 4002 Basel > tel: +41-61-6885469 > fax: +41-61-6882139 > www.basileapharma.com > > > > -= 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 > > > > > >