From ccl@www.ccl.net Fri Jan 17 17:54 EST 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id RAA11840; Fri, 17 Jan 1997 17:54:57 -0500 (EST) Received: from xray5.chem.louisville.edu for dew01@xray5.chem.louisville.edu by bedrock.ccl.net (8.8.3/950822.1) id RAA16183; Fri, 17 Jan 1997 17:54:57 -0500 (EST) Received: (from dew01@localhost) by xray5.chem.louisville.edu (950413.SGI.8.6.12/950213.SGI.AUTOCF) id RAA29101 for chemistry@ccl.net; Fri, 17 Jan 1997 17:58:35 -0500 Date: Fri, 17 Jan 1997 17:58:35 -0500 From: dew01@xray5.chem.louisville.edu (Donald E. Williams) Subject: Software available for LSQ Fit of ESP Message-Id: <199701172258.RAA29101@xray5.chem.louisville.edu> To: chemistry@ccl.net SOFTWARE AVAILABILITY ANNOUNCEMENT Pdm97, Least-Squares Fitting of the Molecular Electrostatic Potential With Net Atomic Charges and/or Multipoles Reliable net atomic charges/multipoles can be found by fitting the molecular electric potential with program pdm97. The program provides a choice of geodesic(1), Connolly(2), cubic(3), or user specified grid points for the electric potential. The program includes calculation of hyperbolic-restricted charge magnitudes(4). In addition to net atomic charges, the program also allows any combination of atomic dipoles/quadrupoles, bond dipoles, as well as the addition of lone pair electron sites if required. The program directly reads output files from Gaussian-92 and Gaussian-94 programs, and will accept edited input from any program which produces a molecular electric potential on a grid. Program pdm97 is the most complete and versatile software package available for this type of calculation. Molecular interactions occur during host-substrate docking, cluster, and crystal formation - whenever molecules associate with one another. The energy and geometry of molecular association is determined by the force field. As a component of the force field, an accurate set of net atomic charges is required. Or, if higher accuracy is needed, pdm97 can make extensions to the net atomic charge model in a variety of ways. A particularly useful feature of the program is the easy and transparent way in which fixed charges and charge dependency conditions are specified. By specifying appropriate charge dependencies (e.g., equal charges or equal sums of charges), chemical intuition can assist to produce charges which are transferable between related types of molecules or molecular ions. Hyperbolic- restricted charges are specifically designed to increase charge transferability. All charge calculation include a complete error treatment with standard deviations and correlations between variables. References (1) Spackman, M. A., "Potential Derived Charges Using a Geodesic Point Selection Scheme", J. Comput. Chem 1996, 17, 1-18 (2) Connolly, M. L., "Solvent-accessible Surfaces of Proteins and Nucleic Acids", Science 221, 709-713 (1983) (3) Williams, D. E., "Net Atomic Charge and Multipole Models for the Ab Initio Molecular Electric Potential", Rev. Comp. Chem. 1991, 2, 219-271. (4) Bayly, C. L.; Cieplak, P.; Cornell, W. D.; Kollman, P. A., "A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model", J. Phys. Chem. 1993, 97, 10269-10280. For further information contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA. E-mail:dew01@xray5.chem.louisville.edu Tel:(502)852-5975 Fax:(502)852-8149 From ccl@www.ccl.net Sat Jan 11 02:15:30 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id BAA23108; Sat, 11 Jan 1997 01:21:05 -0500 (EST) Received: from voimax.voima.jkl.fi for eloranta@voimax.voima.jkl.fi by bedrock.ccl.net (8.8.3/950822.1) id BAA21579; Sat, 11 Jan 1997 01:21:05 -0500 (EST) Received: (from eloranta@localhost) by voimax.voima.jkl.fi (8.8.4/8.8.4) id IAA00083 for chemistry@ccl.net; Sat, 11 Jan 1997 08:21:09 +0200 From: Jussi Eloranta Message-Id: <199701110621.IAA00083@voimax.voima.jkl.fi> Subject: Re: CCL:viewmol question????? To: chemistry@ccl.net Date: Sat, 11 Jan 1997 08:21:09 +0200 (EET) In-Reply-To: from "Markus Dickebohm" at Jan 11, 97 03:44:56 am Content-Type: text >No, you are perfectly right: "viewmol" _is_ dependent on Motif. Maybe >you can give LessTif a try to compile viewmol -- many applications run >happily with Lesstif (a free Motif clone) dynamically linked. > I have already tried this. It didn't work. However if you have shared image of motif (distributed by some commercial package) then you can use the lesstiff include files to compile it ;-) (this applies to motif 1.2 because viewmol was compiled with motif 2.0). Also is anyone working on gaussian 94 support? At least the normal modes were not read in correctly since there are differences between the g92 and g94. BTW is this sort of info stored in the checkpoint file too? (but then there are probably byte ordering & float format probelms among various machines). Regards, Jussi Eloranta From ccl@www.ccl.net Wed Jan 15 10:16:32 1997 Received: from bedrock.ccl.net for ccl@www.ccl.net by www.ccl.net (8.8.3/950822.1) id KAA23605; Wed, 15 Jan 1997 10:15:07 -0500 (EST) Received: from pscuxa.psc.edu for dobler@psc.edu by bedrock.ccl.net (8.8.3/950822.1) id KAA10881; Wed, 15 Jan 1997 10:15:05 -0500 (EST) Received: (from dobler@localhost) by pscuxa.psc.edu (8.8.4/8.7.3 PSC 1996/02/27 lambert) id KAA21669; Wed, 15 Jan 1997 10:15:04 -0500 Date: Wed, 15 Jan 1997 10:15:03 -0500 (EST) From: Stephanie Dobler To: chemistry@ccl.net Subject: CCL: ANNOUNCE: Supercomputing Techniques Workshop Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII The following is a workshop announcement that we hope you can include. Please feel free to edit if it's too long. Thanks very much. Stephanie Dobler Education Assistant Pittsburgh Supercomputing Center Pittsburgh Supercomputing Center Supercomputing Techniques: CRAY J90/C90 March 24-27, 1997 -------------------------------------------------------------------------------- REGISTRATION DEADLINE: March 3, 1997 -------------------------------------------------------------------------------- PURPOSE: The purpose of this three and a half day workshop is to introduce participants to computing on the CRAY J90/C90. Participants will gain experience in running jobs on the J90/C90, optimizing code, parallel processing, and on the use of graphics software libraries and packages. AGENDA: The first day of this workshop is designed to introduce participants to the J90/C90 platform. During this time, participants will become familiar with PSC's supercomputing environment, the UNICOS operating system, CRAY compiling, job submission, troubleshooting, and debugging. The last three days of this workshop are designed for users who are already familiar with running jobs on the CRAY J90/C90 and who are interested in more advanced topics: * The Code Optimization portion will cover performance monitoring techniques and strategies to improve the performance of one's code. * The Parallel Processing portion concentrates on the mechanics of parallel computing on the J90/C90 systems. * The final day will explore graphics and visualization topics ranging from a general overview of graphics packages available at PSC to a more advanced discussion of animation and 3-D graphics. To ensure that participants receive quality training, our workshops incorporate both lectures and extensive hands-on lab sessions. Programming exercises are carefully designed to reinforce concepts and techniques taught in class. Our instructors have strong scientific and technical backgrounds and are available for individual consultation during lab sessions. In addition to the lab exercises, lab time will also be available for participants to optimize their own code with the help and supervision of our instructors. Participants are encouraged to bring their code, but not required. ==> A working knowledge of FORTRAN or C and UNIX are required. REGISTRATION FEES: Admission to this training workshop is free to the United States academic community. Interested corporate and government applicants, as well as applicants from academic institutions outside the United States should contact Kathi Burgard at (412) 268-5131 for information on attendance fees. HOUSING AND TRAVEL: Housing and travel are the responsibility of participants, but we will provide information on local hotels at your request. Group rates for local hotels are available on a first-come, first-served basis. REGISTRATION: To register for Supercomputing Techniques: CRAY J90/C90, please complete and return the application form below by March 3, to: Workshop Application Committee ATTN: Kathi Burgard Pittsburgh Supercomputing Center 4400 Fifth Avenue, Pittsburgh, PA 15213. You may also apply for this workshop by sending requested information via electronic mail to workshop@psc.edu or via fax to (412/268-5832). All applicants will be notified of acceptance during the week of March 3, 1997. For additional online information, including a preliminary agenda, please visit the workshop's homepage: http://www.psc.edu/training/J90_Mar_97/welcome.html =============================================================================== Name: Please circle one: Ms. Mr. Dr. Prof. Department: Univ/Ind/Gov Affiliation: Address: Telephone: W ( ) H( ) Electronic Mail Address: Social Security Number: Citizenship: Are you a PSC user (yes/no)? If yes, please give your PSC username: Academic Standing (please check one): F - Faculty UG - Undergraduate I - Industrial PD - Postdoctorate UR - University Research Staff GV - Government GS - Graduate Student UN - University Non-Research Staff O - Other Please explain why you are interested in attending this workshop and what you hope to gain from it. Briefly describe your computing background (scalar, vector, and parallel programming experience; platforms; languages) and research interests. Please indicate the workshop for which you are applying: The following information is OPTIONAL and is for statistical reporting only. Ethnic origin: ___African American ___Hispanic ___Asian or Pacific Islander ___Caucasian ___American Indian or Alaskan Native ___Other (please specify) Sex: ___Male ___Female All applicants will be notified of acceptance during the week of March 3. From morokuma@euch4e.chem.emory.edu Thu Jan 16 13:30:47 1997 Received: from euch4e.chem.emory.edu for morokuma@euch4e.chem.emory.edu by www.ccl.net (8.8.3/950822.1) id MAA02681; Thu, 16 Jan 1997 12:53:52 -0500 (EST) From: Received: by euch4e.chem.emory.edu (AIX 3.2/UCB 5.64/4.03) id AA24661; Thu, 16 Jan 1997 12:53:52 -0500 Message-Id: <9701161753.AA24661@euch4e.chem.emory.edu> Subject: Emory Undergraduate Research Program To: chemistry@www.ccl.net Date: Thu, 16 Jan 1997 12:53:52 -0500 (EST) X-Mailer: ELM [version 2.4 PL24] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit UNDERGRADUATE SUMMER RESEARCH FELLOWSHIP PROGRAM In Computational Chemistry & Physics June 9-August 15, 1997 Cherry L. Emerson Center For Scientific Computation EMORY UNIVERSITY Atlanta, Georgia, USA OBJECTIVE Provide intensive research training in computational chemistry/physics including electronic structures, molecular dynamics and modeling; gain experience using an IBM SP2 supercomputer and IBM RS6000 workstations; all of which, will enhance the student's career development in computational chemistry and physics. Fellows will pursue individual research projects under the direction of faculty members associated with the Center. Lectures, seminars by faculty, and student seminars will supplement the research program. QUALIFICATONS Completion of junior undergraduate year with a major in chemistry or physics. Criteria used in determining fellowship will include college grades, relevant experience and interest, and letters of recommendation from faculty members. SPECIAL FOR THIS YEAR This summer will be exceptional, in that, the 9th International Congress of Quantum Chemistry, the most important international conference in quantum chemistry, will be held at the Emory Conference Center from June 9-14, 1997. The first week of the undergraduate program will be devoted to attending the Congress and getting aquainted with the frontiers in computational chemistry. APPLICATION DEADLINE March 31, 1997 STIPEND $3500/10 week program. Up to $300 towards travel expenses is available upon request. HOUSING Double room occupancy is available for approx. $15/night and would be deducted from stipend. WEB SITE More details of the Emerson Center and the Undergraduate Summer Research Fellowship Program in Computational Chemistry & Physics can be found at our web site: http://www.emerson.emory.edu/ TO APPLY, 1. Go to the web site above and get the necessary information and forms, 2. or contact: Professor Keiji Morokuma, Director Cherry L. Emerson Center for Scientific Computation Emory University 1515 Pierce Drive Atlanta, Georgia 30322 Phone: (404) 727-2380 Fax: (404) 727-6586 E-mail: clec@euch3g.chem.emory.edu Emory University is an equal opportunity/affirmative action employer From ragno@naxos.caspur.it Fri Jan 17 03:16:57 1997 Received: from mail.caspur.it for ragno@naxos.caspur.it by www.ccl.net (8.8.3/950822.1) id CAA05619; Fri, 17 Jan 1997 02:42:59 -0500 (EST) Received: from naxos.caspur.it (naxos.caspur.it [193.204.5.8]) by mail.caspur.it (8.8.4/8.8.4) with ESMTP id IAA23158; Fri, 17 Jan 1997 08:41:21 +0100 Received: from localhost (ragno@localhost) by naxos.caspur.it (8.8.4/8.8.4) with SMTP id IAA16009; Fri, 17 Jan 1997 08:41:20 +0100 (MET) Date: Fri, 17 Jan 1997 08:41:20 +0100 (MET) From: Gianluca Sbardella Reply-To: Gianluca Sbardella To: orgchem-l cc: "Thomas R. Harrer" , chemistry@www.ccl.net, ANCHODD , Multiple recipients of List , Structural NMR Mail List Subject: Is OrgChem still "alive" ??? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters, I'm sending this question to a few different mail lists: my apologies for any repetitiion!!! The question is this: Does anybody know if ORGCHEM (Organic Chemistry Mail List) IS STILL ALIVE? Thank you all in advance, Gianluca Sbardella *************************************************************** * * * Dr. Gianluca Sbardella E-mail: r.ragno@caspur.it * * Dip. Studi Farmaceutici * * Universita' "La Sapienza" Phone: 39-6-49913814 * * P.le A. Moro, 5 Fax: 39-6-491491 * * 00185 Roma * * ITALY * * * *************************************************************** From Jeffrey.Nauss@UC.Edu Fri Jan 17 11:17:01 1997 Received: from blues.fd1.uc.edu for Jeffrey.Nauss@UC.Edu by www.ccl.net (8.8.3/950822.1) id LAA07864; Fri, 17 Jan 1997 11:06:21 -0500 (EST) Received: from beryllium.crs.uc.edu by UCBEH.SAN.UC.EDU (PMDF V5.0-7 #15949) id <01IEBFEZTK8SH129NS@UCBEH.SAN.UC.EDU>; Fri, 17 Jan 1997 10:57:50 -0500 (EST) Received: by beryllium.crs.uc.edu (951211.SGI.8.6.12.PATCH1042/940406.SGI.AUTO) id KAA05438; Fri, 17 Jan 1997 10:58:15 -0500 Date: Fri, 17 Jan 1997 10:58:13 -0500 From: Jeffrey.Nauss@UC.Edu (Jeffrey L. Nauss) Subject: Summary: Removing charges for an MD simulation To: DIBUG@sunsite.icm.edu.pl, chemistry@www.ccl.net Reply-to: Jeffrey.Nauss@UC.EDU Message-id: <9701171058.ZM5436@beryllium.crs.uc.edu> Organization: Dept. Chemistry, University of Cincinnati MIME-version: 1.0 X-Mailer: Z-Mail (3.2.2 10apr95 MediaMail) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7BIT X-Zm-Priority: Low Recently, I sent out the following post: +++++++++++ BEGIN ORIGINAL MESSAGE ++++++++++++++++ One of the problems one has in MD simulations is that long runs must be performed to see anything significant, for example, and in my specific case, determination of NMR order parameters or conformational searches. Performing the run in explicit solvent with periodic boundary conditions is undoubtably the best way to perform the simulations. However, these simulations require large amounts of CPU time and disk space for the large history files. To get around these problems, people have run simulations in vacuo. This was done in the early days of MD simulations but with parameter sets that often took into account the absence of solvent. Furthermore, electrostatic screening was accomplished by using a distance dependent dielectric constant. Still, a continuing problem that I have found during an in vacuo run is the collapse of the molecule. Proteins will shrink (in terms of the radius of gyration) and side chains will fall onto the surface of the protein. Peptides often fold up into themselves. To some extent, this collapse is a result of coulmbic interactions that are not properly shielded. Ornstein's group tried to get around this problem by rendering acidic, basic, N-termini, and C-termini functional groups net neutral (JBSD vol 9, page 935 (1992)). It appeared to be somewhat successful. Has anyone tried MD simulations, particularly with small molecules like peptides and carbohydrates, with a similar approach? I am thinking perhaps of performing the simulation with the Coulombic interactions scaled down or even shut off. Of course, one must assume that the Coulombic interactions will not play a major role in the dynamics. How valid is that assumption will depend on the system studied, I would think. Comments will be appreciated. References will be even better. +++++++++++ END ORIGINAL MESSAGE ++++++++++++++++ There seems to be a fair of amount of thought on the subject. And there seems to be some good results with various techniques. At least enough for me to give it a try. Here is a summary of the responses. Thank you to all who responded. ======================================================================== From: bear@ellington.pharm.arizona.edu (Soaring Bear) Are you aware of the approach of using higher dielectric r? There's been a bit of literature on using 4 instead of 1. I could dig up some refs if you want. >Forgot to mention that. Do you have a ref or two for it? comparison in: J Biomolec Struct & Dynam 11:429-41 1993 nice discussion by Daggett/Kollman: Biopolymers 31:285-304 1991 Chemica Scripta 29a:205-15 1989 mathematic treatment by Ramachandran: Indian J Biochem 7:95-7 1970 ======================================================================== From: D.van.der.Spoel@chem.rug.NL A conservative answer, just use the solvent and save yourself a lot of trouble justifying simulations without solvent. You can do nanosecond simulations of a protein in water on a reasonable workstation, or even a Pentium Pro PC. If performance is crucial, check out the GROMACS software, it is probably the fastest MD code on workstations. http://rugmd0.chem.rug.nl/~gmx ======================================================================== From: Peter Grootenhuis I fully appreciate the problem you described with long MD runs. It inspired us to generate a CHARMm-based force field for carbohydrates (CHEAT95) in which the effect of solvent is implicitly included. We also performed several MD-runs and typically got good results. The references are: Grootenhuis & Haasnoot, Mol.Simul. 10 (1993) 75-95 and Kouwijzer & Grootenhuis, J. Phys. Chem 99 (1995) 13426-13436 The CHEAT95 force field is available at: http://www.msi.com/support/quanta/cheat95.html ======================================================================== From: John Liebeschuetz We've, in the past, carried out a number of in vacuo simulations of drug/DNA complexes. No counterions were included so we scaled the phosphate charges to -0.25 to simulate counterion shielding. This figure was rather ad hoc but seemed to give reasonable results. Some of the ligands examined were cationic. These were scaled to a charge of +0.5 over the whole molecule and again seemed to give good results. In most of these simulations we still had to restrain the DNA to stop it collapsing. The charges on the cationic ligand were originally ESP calculated in AM1. We could have just halved the charges on each atom but we wanted to maintain the charge differentials between electropositive and electronegative atoms. This was done by carrying out the AM1 calculation on the unprotonated and protonated species and then averaging the charges on each atom. The charge on the extra proton was just halved. > Have you a reference for this work? Not for cases where the charges were partially removed. I do have one however for a case where the DNA phosphates were made neutral. N.L.Fregeau, Y. Wang, R.T.Pon, W.A.Wylie & J.W.Lown, J. Amer. Chem. Soc., 117 (1995), 8917-8925. > Did you manipulate the partial charges on the atoms to arrive at this scaled > down value or did you scale all Coulombic interactions? for DNA, the charges on the DNA phosphate oxygens only were scaled down. The charge on each atom was reduced by a quantity proportional to the original negative charge. This method was used whether the group was to be partially or fully neutralised. The ligand was treated differently. When the ligand cationic charge was scaled according to the method I described, the net effect was to alter atomic charges in the vicinity of the cation centre only. ======================================================================== From: Pieter Stouten >Ornstein's group tried to get around this problem by rendering acidic, >basic, N-termini, and C-termini functional groups net neutral (JBSD >vol 9, page 935 (1992)). It appeared to be somewhat successful. > GROMOS has had a force field with net neutral groups for vacuum simulations at least since 1984 (when I started using it), but probably much longer. It definitely works better than full-blown charges. See e.g.: D.M.F. van Aalten, A. Amadei, R.P. Bywater, J.B.C. Findlay, H.J.C. Berendsen, C. Sander & P.F.W. Stouten, "A Comparison of Structural and Dynamic Properties of Different Simulation Methods Applied to SH3," Biophys. J. 70 (1996) 684-692. We also found that stochastic dynamics (SD, with friction and random "kicks") worked better than straight MD. We also tried a simplistic continuum solvation term described in: P.F.W. Stouten, C. Froemmel, H. Nakamura & C. Sander, "An Effective Solvation Term Based on Atomic Occupancies for Use in Protein Simulations," Mol. Simulation 10 (1993) 97-120. That method is computationally cheap (20-50% increase in CPU time with respect to vacuum simulations), did work well in BPTI simulations (in fact, when I redid the simulations and was more careful in generating the starting configuration the results were better even than published in the paper), but not so well in the SH3 simulations. ======================================================================== From: Mark D Shenderovich I have discussed similar problems with fellow molecular modelers working with peptides and proteins. I don't know a reference that compares different electrostatic approximations in a systematic way, but I can share with you results of our discussions and my own experience. Charged groups of peptides in water are hydrated and interact through a medium of a high dielectrics. Using charged states of terminal and side chain groups in vacuo tremendously overestimates their electrostatic interactions and causes the collapse you've described. The charged groups tend to form salt bridges or multi-H-bond networks. To my experience, a distance dependent dielectrics makes the situation even worse since it stronger punishes separation of opposite charges. You may try a continuum solvation model which would increase CPU time by a reasonable factor of 2-5 and will not require additional disk space. I don't know which software you use, but several commercial packages include a continuum solvation. Although most of these models are poorly parametrized for charged species, it is better than nothing. Second, it is always safer to use neutral form of ionizable groups, both in vacuo and with an "envelope" hydration models (i.e. those which do not calculate effective dielectric constants). If you prefer simulations in vacuo, use a higher dielectric constant (4 to 10) with neutral groups, or a distance dependent dielectric with a coefficient around 4.0. I cannot prove these numbers, they came from my and my colleagues' experience. Also, if possible with your software, use aliphatic hydrogen parameters for neutral COOH groups. This is recommended by people from Scheraga's group to avoid excessive H-bonding of carboxyl. Finally, for conformational searches related to NMR data I often use a continuum dielectric constant of the solvent (80 for water, 45 for DMSO) with charged ionizable groups. Of course, this reduces electrostatics for neutral groups inside the peptide/protein, but they ether don't play a major role in intramolecular interactions or not vary much from one conformation to another. ======================================================================== From: JAQ@XRAY.BMC.UU.SE I saw you ccl-posting. You might find the references J. Mol. Biol. (1985) 183: 461 and Biopolymers (1990) 30: 205 useful. We looked at some of the issues you mention there, and there may be some other useful references for you as well. ======================================================================== From: "Thomas M O'Connell" We recently published a study on the helix-coil transition for short peptides that may be of interest to you. In this study we ran dynamics/free energy simulations in vacuo with the dielectric constant set to 5, 25 and infinity (i.e. all charges turned off). This of course had definite effects on the thermodynamics of the peptide conformation and folding. The reference is : Wang, O'Connell, Tropsha and Hermans Biopolymers 39, 479 (1996) Also of interest is a study that came out a while ago from Bernie Brooks in which he ran some dynamics on BPTI (if I remember correctly) in which all charges were removed. I can't seem to find this in my files so you'll have to do a search, but not surprizingly the folded system was stable. ======================================================================== From: case@riscsm.scripps.EDU (David Case) We've thought a lot about doing this, but for some reason have never actually tried it....For peptides, some models of solvation effects almost perfectly cancel out the conformational dependence of the electrostatic term, i.e. the sum of the (gas-phase) electrostatic term and the solvation term is nearly constant as a function of conformations sampled during a solvated MD run. So it's certainly not a crazy idea. No references yet, but we have a couple of papers submitted on this subject. ======================================================================== -- Jeff Nauss *********************************************************************** * UU UU Jeffrey L. Nauss, PhD * * UU UU Director, Molecular Modeling Services * * UU UU Department of Chemistry * * UU UU CCCCCCC University of Cincinnati * * UU UU CCCCCCCC Cincinnati, OH 45221-0172 * * UUUU CC * * CC Telephone: 513-556-0148 Fax: 513-556-9239 * * CC * * CCCCCCCC e-mail: Jeffrey.Nauss@UC.Edu * * CCCCCCC URL http://www.che.uc.edu/~nauss * *********************************************************************** From kelterer@fptchbds01.tu-graz.ac.at Mon Jan 20 05:17:33 1997 Received: from fptchbds01.tu-graz.ac.at for kelterer@fptchbds01.tu-graz.ac.at by www.ccl.net (8.8.3/950822.1) id EAA26859; Mon, 20 Jan 1997 04:58:05 -0500 (EST) Received: by fptchbds01.tu-graz.ac.at (5.57/Ultrix3.0-C) id AA23192; Mon, 20 Jan 97 11:56:52 +0100 Date: Mon, 20 Jan 97 11:56:52 +0100 From: kelterer@fptchbds01.tu-graz.ac.at (M.Kelterer) Message-Id: <9701201056.AA23192@fptchbds01.tu-graz.ac.at> To: chemistry@www.ccl.net, hinsen@ibs.ibs.fr Subject: Re: CCL:Monte-Carlo calculations on proteins Dear Prof. Hinsen, dear netters, Once again the answers to my question A. Kelterer email: kelterer@fptchbds01.tu-graz.ac.at > I'd like to use the program MMFF94 > -- either in BatchMin version 5.5 from Clark Still's group > -- or the earlier Cerius2 implementation of MMFF93 from MSI. > > Who can help me with the email- or fax-adress of the group > who is distributing these programs, the costs > of the programs and/or experience with performance, > handling, etc ? 1) I can answer a related question; MMFF has been added to the c25 version of CHARMM, which is distributed by the Karplus group at Harvard (for a modest fee; a few hundred dollars, I believe). See http://yuri.harvard.edu -- Rick Venable =====\ |=| "Eschew Obfuscation" FDA/CBER Biophysics Lab |____/ |=| Bethesda, MD U.S.A. | \ / |=| ( Not an official statement or rvenable@deimos.cber.nih.gov \/ |=| position of the FDA; for that, http://nmr1.cber.nih.gov/venable.html |=| see http://www.fda.gov ) --------------------------------------------------------------------------- 2) This was a very good information, costs of MacroModel/Batchmin are us$ 1000. for a single academic license. AMK. Hello, Please see the URL below for info about MacroModel/Batchmin. You can write to us at "mmod@still3.chem.columbia.edu" for further information. -P. -- ************** Watch this space for an important message... *************** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** MacroModel WWW page: http://www.cc.columbia.edu/cu/chemistry/mmod/mmod.html --------------------------------------------------------------------------- 3) From richard@tc.cornell.edu Wed Dec 4 18:43:48 1996 I would like to know this as well. Could you forward the info to me too? Thanks ps. We are developing a C++ class library for automatic assignment and energy evaluation of MMFF94. It will be integrated into a flexible ligand docking code being developed at University of Alberta Canada (but also available as a library). The authors of the docking code are planning on offering a workshop with me (here at Cornell) tentatively scheduled for late April 1997. We will post an official announcement on CCL some time in late January. Richard Gillilan Cornell Theory Center ----------------------------------------------------------------------- From boufer@cennas.nhmfl.gov Mon Jan 20 10:17:36 1997 Received: from cennas.nhmfl.gov for boufer@cennas.nhmfl.gov by www.ccl.net (8.8.3/950822.1) id KAA28330; Mon, 20 Jan 1997 10:11:55 -0500 (EST) Received: (from boufer@localhost) by cennas.nhmfl.gov (8.8.4/8.8.4) id KAA09663 for chemistry@www.ccl.net; Mon, 20 Jan 1997 10:11:58 -0500 (EST) From: Ahmed Bouferguene Message-Id: <199701201511.KAA09663@cennas.nhmfl.gov> Subject: SCF source code To: chemistry@www.ccl.net Date: Mon, 20 Jan 1997 10:11:58 -0500 (EST) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Hi CCL'ers, Need a scf fortran source code. I would be very thankful to anybody who can indicate me a site from which I could get such a program. Thankx From mbdtsnj@afs.mcc.ac.uk Mon Jan 20 11:17:37 1997 Received: from curlew.cs.man.ac.uk for mbdtsnj@afs.mcc.ac.uk by www.ccl.net (8.8.3/950822.1) id KAA28389; Mon, 20 Jan 1997 10:19:09 -0500 (EST) Received: from mchhpb01.ch.man.ac.uk by curlew.cs.man.ac.uk with SMTP (PP); Mon, 20 Jan 1997 14:40:17 +0000 From: mbdtsnj Message-Id: <24512.9701201440@mchhpb01.ch.man.ac.uk> Subject: phospohistidine_parameters To: chemistry@www.ccl.net Date: Mon, 20 Jan 1997 14:40:29 +0000 (GMT) X-Mailer: ELM [version 2.4 PL24alpha3] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear CCLers, I am currently attempting to study a phosphorylated histidine residue:- -C O \ | N-P-O-H / | -C O Using the Weiner et.al. MM force field. I am unable to find parameters in any standard database or in the literature. If anyone has parameters for this or a sufficiently similar system I would be eternally grateful for any assistance. I am missing C-N-P and N-P-O angle parameters and C-N-P-O torsional parameters. Thank-you Nick Jones(mbdtsnj@afs.mcc.ac.uk) Dept. of Chemistry University of Manchester UK From ep7@dent.okayama-u.ac.jp Mon Jan 20 22:17:42 1997 Received: from deews1.dent.okayama-u.ac.jp for ep7@dent.okayama-u.ac.jp by www.ccl.net (8.8.3/950822.1) id VAA01504; Mon, 20 Jan 1997 21:47:02 -0500 (EST) From: Received: from [150.46.140.80] (yobou2.dent.okayama-u.ac.jp [150.46.140.80]) by deews1.dent.okayama-u.ac.jp (8.7.5+2.6Wbeta6/3.3W9) with SMTP id LAA20479 for ; Tue, 21 Jan 1997 11:48:20 +0900 (JST) Message-Id: <199701210248.LAA20479@deews1.dent.okayama-u.ac.jp> Date: Tue, 21 Jan 1997 11:49:29 +0900 To: CHEMISTRY@www.ccl.net X-Sender: ep7@dent.okayama-u.ac.jp (Unverified) Subject: Re: CCL: Electron correlation MIME-Version: 1.0 Content-Type: text/plain; charset=iso-2022-jp X-Mailer: Eudora-J(1.3.8.5-J13) I have the answers for the following question: I ask everybody about the books and reviews for electron correlation. I thank everybody. I summarize the answers. Masao Masamura Preventive Dentistry Okayama University Dental School Shikata-cho, 2-5-1 Okayama 700 Japan FAX: 81-86-225-3724 e-mail: ep7@dent.okayama-u.ac.jp From: "Jens Spanget-Larsen" Organization: Roskilde Universitetscenter To: Date: Wed, 8 Jan 1997 08:51:26 +0100 Subject: CCL:Electron correlation Priority: normal X-Mailer: Pegasus Mail for Windows (v2.42a) Masao Masamura: > I ask everybody about the books and reviews for electron correlation. Three recent review papers in JPC vol.100 are highly relevant: M. Head-Gordon: "Quantum Chemistry and Molecular Processes" J. Phys. Chem. 100, 13213-13225 (1996) K. Raghavachari, J.B. Anderson: "Electron Correlation Effects in Molecules" J. Phys. Chem. 100, 12960-12973 (1996) W. Kohn, A.D. Becke, R.G. Parr: "Density Functional Theory of Electronic Structure" J. Phys. Chem. 100, 12974-12980 (1996) Numerous additional references to the subject are given in these papers, in particular in the one by Raghavachari and Anderson (187 references). Good Luck! Yours, Jens >--< =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= JENS SPANGET-LARSEN Department of Chemistry Phone: +45 46757781 + 2710 Roskilde University (RUC) Fax: +45 46757721 P.O.Box 260 E-Mail: JSL@virgil.ruc.dk DK-4000 Roskilde, Denmark http://frederik.ruc.dk/dis/chem/psos =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Date: Wed, 8 Jan 1997 09:25:46 -0500 (EST) From: Jeff Stephens X-Sender: jeffs@gobryas.ccqc.uga.edu To: ep7@dent.okayama-u.ac.jp Subject: Re: CCL:Electron correlation Content-Type: TEXT/PLAIN; charset=US-ASCII Methods In Computational Chemistry 1: Electron Correlation in Atoms and Molecules edited by Stephen Wilson -Jeff Stephens Date: Wed, 8 Jan 1997 09:25:46 -0500 (EST) From: Jeff Stephens X-Sender: jeffs@gobryas.ccqc.uga.edu To: ep7@dent.okayama-u.ac.jp Subject: Re: CCL:Electron correlation Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 9 Jan 1997 14:42:43 +0100 (MET) From: Robert Franke To: ep7@dent.okayama-u.ac.jp Subject: electron correlation Content-Type: TEXT/PLAIN; charset=US-ASCII dear masao, one of the best overviews about literature concerning ab initio methods and naturally also literature concerning correlation is in my opinion the booklet of H.F. Schaefer III: Quantum Chemistry The development of ab initio methods in molecular electronic structure theory Clarendon Press, Oxford, 1984 It is a commented list of landmark papers from 1928 till 1983. From: andrus@boc.ic.ee (Andrus Metsala) X-Mailer: SCO System V Mail (version 3.2) To: ep7@dent.okayama-u.ac.jp Subject: RE: Electron correlation Date: Fri, 10 Jan 97 11:53:02 estonia Hello Masao Masamura: > I ask everybody about the books and reviews for electron correlation. > > Please replay to me. > > Thank you in advance. I know two good resource about electron correlation: R.C.McWeeny, B.T.Sutcliffe, Methods of Molecular Quantum Mechanics, Academic Press, London, 1969. S.Wilson, Electron Correlation in Molecules, Clarendon Press, Oxford, 1984 Sincerely, yours ________________________________________________________________________ Andrus Metsala Phone: (3722)526510 Institute of Chemistry Fax: (3722)536371 Estonian Academy of E-Mail: andrus@boc.ic.ee Sciences Akadeemia tee 15 EE0026 Tallinn Estonia _________________________________________________________________________ Date: Fri, 17 Jan 1997 10:38:05 -0500 From: Boyd Subject: electron correlation To: "Masamura, Masao" X-Mailer: Mail*Link SMTP-MS 3.0.2 Content-transfer-encoding: 7BIT Dear Dr. Masamura, Last week you were asking about books and chapters on electron correlation. Did you get the information you needed? You may wish to look at the chapter by Rod Bartlett on post-Hartree-Fock methods in Volume 5 (1994) of Reviews in Computational Chemistry. It is very good and has been used in the classroom. Good luck, Don Boyd REVIEWS IN COMPUTATIONAL CHEMISTRY Home Page on the World Wide Web URL http://chem.iupui.edu/~boyd/rcc.html