From brock@chemie.uni-hamburg.de Tue Dec 21 05:19:18 1993 Received: from deneb.dfn.de for brock@chemie.uni-hamburg.de by www.ccl.net (8.6.4/930601.1506) id EAA01572; Tue, 21 Dec 1993 04:35:29 -0500 Received: from fbihh.informatik.uni-hamburg.de by deneb.dfn.de (4.1/SMI-4.2) id AA00503; Tue, 21 Dec 93 10:32:55 +0100 Received: from ocws1.chemie.uni-hamburg.de by fbihh.informatik.uni-hamburg.de (5.65+/FBIHH-1.25) with SMTP; id AA18167; Tue, 21 Dec 93 10:33:04 +0100 Received: by ocws1.chemie.uni-hamburg.de (AIX 3.2/UCB 5.64/4.50) id AA14834; Tue, 21 Dec 1993 10:22:01 +0100 From: brock@chemie.uni-hamburg.de (Mathias Brock) Message-Id: <9312210922.AA14834@ocws1.chemie.uni-hamburg.de> Subject: DBWS-9006 source wanted To: chemistry@ccl.net Date: Tue, 21 Dec 1993 10:21:57 +0100 (MEZ) Cc: brock@chemie.uni-hamburg.de (Mathias Brock) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 361 Dear netters, I am looking for software for Rietveld refinement on UNIX or MSDOS machines in source code, namely FORTRAN or C. A Standard programm is DBWS-9006. If anybody knows about a public domain version and the way of delivery I would be grateful for your help. Answers to brock@chemie.uni-hamburg.de. Best wishes, Mathias brock@chemie.uni-hamburg.de From grfamini@cbdcom.apgea.army.mil Tue Dec 21 07:19:17 1993 Received: from cbdcom.apgea.army.mil for grfamini@cbdcom.apgea.army.mil by www.ccl.net (8.6.4/930601.1506) id HAA02266; Tue, 21 Dec 1993 07:07:52 -0500 Date: Tue, 21 Dec 93 7:05:56 EST From: George R Famini To: chemistry@ccl.net Subject: SMILES -> Molfile Message-ID: <9312210705.aa27684@cbdcom.apgea.army.mil> Hello All, A friend of mine out in industry is interested in getting a PC based program that converts smiles notation into molfiles. It is not necessary there be graphics, and all he is interested in is a 2d representation (for inclusion into ISIS). Does anybody out there know of anything that would be applicable (but isn't too expensive, free would, of course be preferred). Thanks George R. Famini From holcombr@pr.cyanamid.com Tue Dec 21 10:19:22 1993 Received: from primail.pr.cyanamid.com for holcombr@pr.cyanamid.com by www.ccl.net (8.6.4/930601.1506) id JAA03407; Tue, 21 Dec 1993 09:56:21 -0500 Message-Id: <199312211456.JAA03407@www.ccl.net> Date: Tue, 21 Dec 93 09:56:22 -0500 From: "Ryan C. Holcomb" To: chemistry-request@ccl.net, chemistry@ccl.net Subject: Re: SMILES -> Molfile The application Chameleon by ConSystant provides on-the-fly conversion betwe  various format types including SMILES and Molfile. The version for the Mac wor  works well by converting the clipboard information as you cross over between applications such as ChemDraw and ISIS-Base. There is a little overhead but it is worth it. I believe the PC version is available as well. Ryan Holcomb, Senior Research Scientist Oncology and Immunology Research American Cyanamid Company Lederle Laboratories Pearl River, NY 10965 Phone:(914) 732-2499 E-mail: holcombr@pr.cyanamid.com From MMADRID@B.PSC.EDU Tue Dec 21 10:36:46 1993 Received: from B.PSC.EDU for MMADRID@B.PSC.EDU by www.ccl.net (8.6.4/930601.1506) id KAA03447; Tue, 21 Dec 1993 10:06:06 -0500 From: Date: Tue, 21 Dec 1993 10:06:05 -0500 (EST) To: chemistry@ccl.net Message-Id: <931221100605.20412091@B.PSC.EDU> Subject: nucleic acid and protein sequence workshop NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS Pittsburgh, Pennsylvania May 29-June 3, 1994 Pittsburgh Supercomputing Center (PSC) is offering a five-day workshop on "Nucleic Acid and Protein Sequence Analysis," May 29-June 3, 1994. It is funded by a grant from the National Center for Human Genome Research of the National Institutes of Health. The workshop will familiarize biomedical researchers with computational methods and provide practice in applying supercomputing resources to problems of concern in macromolecular sequence analysis. Emphasis will be on alignment of and pattern extraction from multiple sequences. Participants will gain practical experience on PSC's Cray C-90 and T3D in (1) comparing and aligning sequences, (2) identifying informative patterns in a set of sequences, and (3) using extracted informative patterns to identify related sequences. Researchers will also learn several approaches to database searching and multiple sequence alignment, how to use profile analysis effectively, and how to identify patterns in their sequences. Participants are encouraged to bring sequence analysis problems from their current research. Extensive documentation will be given at the outset on the VAX/VMS and UNICOS operating systems as well as on the specific programs to be employed in the workshop. No prior supercomputing experience is required. Workshop leaders are Dr. Gary Churchill, Cornell University, and Dr. Michael Gribskov, San Diego Supercomputing Center. A limited number of grants to cover travel and hotel accommodations are available for U.S. academic participants. ALL PARTICIPANTS ARE REQUIRED TO PAY A $135 REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. The deadline for submitting applications is March 31, 1994. Enrollment is limited to 20 participants. An application form is below. Grants of supercomputing time to allow biomedical researchers to explore the appropriateness of supercomputing for their computational problems are available through a program funded by the Biomedical Research Technology Program, National Center for Research Resources, National Institutes of Health. * * * * * PITTSBURGH SUPERCOMPUTING CENTER NUCLEIC ACID AND PROTEIN SEQUENCE ANALYSIS WORKSHOP FOR BIOMEDICAL RESEARCHERS May 29-June 3, 1994 APPLICATION Name: ________________________________________________________________ Affiliation: ________________________________________________________________ Address: ________________________________________________________________ (Business) ________________________________________________________________ ________________________________________________________________ (Home) ________________________________________________________________ Telephone: ____________________________ ______________________________ (Business) (Home) *Social Security Number: _______-_____-_______ Citizenship:___________________ Electronic Mail Address:_______________________________________________________ Status: ___Graduate ___Post-doctoral Fellow ___Faculty ___Other (specify) In order to attend the workshop, will you need funds for travel?___ lodging?___ Please indicate specifically any special housing, transportation or dietary arrangements you will need: __________________________________________ How did you learn about this workshop:_________________________________________ REQUIREMENTS: Applicants must submit a completed application form and a cover letter. The letter should describe, in one or two paragraphs, the sequence analysis problems encountered in your research, and how participating in the workshop will enhance this research. Please include a brief statement describing your level of experience with computers. Faculty members, staff and post-docs should provide a curriculum vita. Graduate students must have a letter of recommendation from a faculty member. If you have requested travel funds, please include the cost of roundtrip air fare from your home to Pittsburgh and indicate the amount of travel funds you will need. ALL PARTICIPANTS WILL BE REQUIRED TO PAY A $135 REGISTRATION FEE UPON ACCEPTANCE INTO THE WORKSHOP. Please return all application materials by MARCH 31, 1994 to: Biomedical Workshop Applications Committee Pittsburgh Supercomputing Center 4400 Fifth Avenue Pittsburgh, PA 15213 Direct inquiries to: Nancy Blankenstein, 412/268-4960, or send electronic mail to blankens@psc.edu. *Disclosure of Social Security Number is voluntary. PSC does not discriminate on the basis of race, color, religion, sex, age, creed, national or ethnic origin, or handicap. From ivar@chem.ut.ee Tue Dec 21 13:19:27 1993 Received: from piko.chem.ut.ee for ivar@chem.ut.ee by www.ccl.net (8.6.4/930601.1506) id MAA06349; Tue, 21 Dec 1993 12:20:56 -0500 Received: by piko.chem.ut.ee (Smail3.1.27.1 #2) id m0pCAlP-0001eyC; Tue, 21 Dec 93 19:20 EET Message-Id: Subject: Mopac 6.0 To: chemistry@ccl.net Date: Tue, 21 Dec 1993 19:20:50 +0200 (EET) From: Ivar Koppel X-Mailer: ELM [version 2.4 PL0] Content-Type: text Content-Length: 237 Sorry, Mopac fans. My ftp server is so dummy /or the lines are so busy that only 1 person can retrive MOPAC-s port to dos at a time. Keep trying and good luck. The best time for that is around noon for States, night for Europe. Ivar From JWANG@ac.dal.ca Tue Dec 21 16:20:38 1993 Received: from ac.dal.ca for JWANG@ac.dal.ca by www.ccl.net (8.6.4/930601.1506) id PAA10215; Tue, 21 Dec 1993 15:44:57 -0500 From: Received: from AC.DAL.CA by AC.DAL.CA (PMDF V4.2-14 #2545) id <01H6QY990PCG003TZS@AC.DAL.CA>; Tue, 21 Dec 1993 16:44:49 -0400 Date: Tue, 21 Dec 1993 16:44:49 -0400 Subject: L-J parameters for Calcium ion To: chemistry@ccl.net Message-id: <01H6QY991RXE003TZS@AC.DAL.CA> X-VMS-To: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT Dear netters, I am trying to do some MD simulations involved Calcium ions, but I cannot find the parameters (sigma and epsiron) of the LJ potential for the ion. Could anyone provide me these parameters or give me a hint so that I can find these data. Also any comment about the simulation of Ca2+ is very welcomed. Thank you and best wishes for the holiday season. Jian Wang Department of Chemistry Dalhousie University Halifax, N.S. Canada B3H 4J3 Tel: (902)-494-7021 Fax: (902)-494-1310 From rrk@iris3.chem.fsu.edu Tue Dec 21 18:19:24 1993 Received: from iris3.chem.fsu.edu for rrk@iris3.chem.fsu.edu by www.ccl.net (8.6.4/930601.1506) id RAA11130; Tue, 21 Dec 1993 17:28:01 -0500 Received: by iris3.chem.fsu.edu (920330.SGI/910603.SGI.RRC04) for CHEMISTRY@ccl.net id AA18539; Tue, 21 Dec 93 17:27:58 -0500 Date: Tue, 21 Dec 93 17:27:58 -0500 From: rrk@iris3.chem.fsu.edu (Randal R. Ketchem) Message-Id: <9312212227.AA18539@iris3.chem.fsu.edu> To: CHEMISTRY@ccl.net Subject: low T epoxy/adhesive Chemistry Netters, I am looking for an epoxy or adhesive that will bond glass to glass at the temperature of liquid nitrogen (-196 C, 77 K). The bond should hold as the glass heats to 40 C. Please email information to: rrk@magnet.fsu.edu Randal R. Ketchem Institute of Molecular Biophysics 904.644.7798 (voice) Florida State University 904.644.8281 (FAX) Tallahassee, FL 32306-3015 rrk@magnet.fsu.edu (email) From stoutepf@chemsci1.es.dupont.com Tue Dec 21 18:21:07 1993 Received: from gatekeeper.es.dupont.com for stoutepf@chemsci1.es.dupont.com by www.ccl.net (8.6.4/930601.1506) id RAA11143; Tue, 21 Dec 1993 17:32:11 -0500 Received: by gatekeeper.es.dupont.com (5.65/ULTRIX-mjr-062991); id AA08845; Tue, 21 Dec 93 17:31:34 -0500 Received: from [138.196.64.95] (chem95.es.dupont.com) by chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com (4.1/SMI-4.1) id AA07305; Tue, 21 Dec 93 17:29:58 EST Message-Id: <9312212229.AA07305@chemsci1.es.dupont.com. chemsci1 chemsci1.es.dupont.com> Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Reply-To: stoutepf@chemsci1.es.dupont.com X-Organization: The Du Pont Merck Pharmaceutical Company X-Mailer: Eudora 1.4 Date: Tue, 21 Dec 1993 17:30:39 -0500 To: JWANG@ac.dal.ca (Jian Wang) From: stoutepf@chemsci1.es.dupont.com (Pieter Stouten) Subject: Re: L-J parameters for Calcium ion Cc: chemistry@ccl.net, dibug@comp.bioz.unibas.ch Hi Jian, >I am trying to do some MD simulations involved Calcium ions, but I cannot >find the parameters (sigma and epsiron) of the LJ potential for the ion. >Could anyone provide me these parameters or give me a hint so that I can >find these data. > Check out: L.J. Bartolotti, L.G. Pedersen & P.S. Charifson, "Long Range Nonbonded Attractive Constants for Some Charged Atoms", J. Comp. Chem., Vol. 12, No. 9, 1125-1128 (1991). These parameters work well in simulations (claims based on FEP calculations of hydration free energies). For calcium it gives C6 = 2.58 kcal A^6/mol and C12 = 35.8 kcal A^12/mol. The paper gives C6 parameters for other metal ions (Li, Na,K,Rb, Cs, Be, Mg, Sr, Ba, Al, Sc, Cr, Mn, Fe, Cu, Zn, Ga, Ge, Se, Ru, Ag, Cd, In, Sn, Eu), too, but not always C12 parameters. However, the authors present a simple scheme to calculate C12 parameters from the corresponding C6 parameters. Hope this helps. Cheers, Pieter. Pieter Stouten, Senior Research Scientist || Computer Aided Drug Design Group || The Du Pont Merck Pharmaceutical Company || Adventures get spoiled P.O. Box 80353, Wilmington, DE 19880-0353 || by being reduced to data Phone: +1 (302) 695 3515 || -- ARA/Fax: +1 (302) 695 4324 || Poul Anderson E-mail: stoutepf@chemsci1.es.dupont.com || Internet Shogi Server: kzinti || From rec@ncifcrf.gov Tue Dec 21 18:21:45 1993 Received: from fcs280s.ncifcrf.gov for rec@ncifcrf.gov by www.ccl.net (8.6.4/930601.1506) id RAA11214; Tue, 21 Dec 1993 17:42:15 -0500 From: Received: from fcindy5.ncifcrf.gov by fcs280s.ncifcrf.gov (4.1/NCIFCRF-3.0/AWF-2.0) id AA04348; Tue, 21 Dec 93 17:34:14 EST Received: by fcindy5.ncifcrf.gov (920330.SGI/911001.SGI) for @fcs280s.NCIFCRF.GOV:chemistry@ccl.net id AA01160; Tue, 21 Dec 93 17:24:34 -0500 Date: Tue, 21 Dec 93 17:24:34 -0500 Message-Id: <9312212224.AA01160@fcindy5.ncifcrf.gov> To: chemistry@ccl.net Subject: MOPAC-DOS Reply-To: cachau@ncifcrf.gov Hi!, For those of you clogging Ivar's machine ;-) here is the address of a reflector site. For those of you that are not aware of what's going on: Ivar Koppel deposited a copy of the executables of MOPAC for DOS on his machine. However, the trafic is too high and the machine keep crashing. You can found a copy of the files in the following reflector: fcindy5.ncifcrf.gov or 129.43.9.58 login "anonymous" and please enter your e-mail address as password. What follows is a transcript of the readme file you will find in the "mopac_dos" subdirectory. Good Luck R.E.Cachau _______________________________________________________________ This directory contain the DOS versions of MOPAC and GO32. What follows is the original e-mail from Ivar Koppel. Any problems with MOPAC please contact Ivar, I'm helping him in the distribution but I had no part in the development of this software. Files in the directory are: MOPAC.EXE & GO32.EXE are the original binary executables MOPAC.EXE.Z & GO32.EXE.Z are the compressed versions of the files. MOPACDOS.ZIP is the pkzipped version (include _both_ files). Please fetch a "compressed" version if you have the tools for decompresion, since that will save quite a bit of bandwidth. If you don't have the tools, it might be a good idea for you to pick the tools in the directory ./pub. _________________________________________________________________ Some weeks ago somebody was interested in MOPAC running under DOS. Now I can say that we have ported MOPAC 6.0 under MSDOS. It can handle currently 38+38 atoms and is basicly the same program as for VMS or IBM (currently only time and date functions are missing i.e date is Today and time is 00 sec). In my 33 Mhz 486 with 4 M RAM it runs as fast as under Linux, compleately in RAM. (No swapping required). It was compiled using DJ Delories Gnu CC port to MSDOS (DJGPP) and f2c compiler. The size of .EXE file is ca 1.3 Mb, the only program you need to run MOPAC is a small program called go32.exe from DJGPP GCC package (free). If you are interested, send E-mail to ivar@chem.ut.ee or peeter@chem.ut.ee. Best regards, Ivar. Ivar Koppel _____________________________________________________________________________ Raul E. Cachau, National Cancer Institute Frederick Cancer Research and Development Center, PRI/DynCorp Structural Biochemistry Program and Frederick Biomedical Supercomputer Center Building 322, Room 19, P.O.Box B, Frederick, MD 21702-1201, USA Phone: +1-(301)-846-6062; Fax: +1-(301)-846-6066; e-Mail: cachau@ncifcrf.gov _____________________________________________________________________________ From shavitt@sodium.mps.ohio-state.edu Tue Dec 21 18:22:21 1993 Received: from sodium.mps.ohio-state.edu for shavitt@sodium.mps.ohio-state.edu by www.ccl.net (8.6.4/930601.1506) id RAA11328; Tue, 21 Dec 1993 17:59:19 -0500 Received: from localhost (shavitt@localhost) by sodium.mps.ohio-state.edu (8.6.4/8.6.4) id RAA04930 for chemistry@ccl.net; Tue, 21 Dec 1993 17:59:18 -0500 Date: Tue, 21 Dec 1993 17:59:18 -0500 From: Isaiah Shavitt Message-Id: <199312212259.RAA04930@sodium.mps.ohio-state.edu> To: chemistry@ccl.net Subject: Questionaire about quantum chemistry ab initio programs Reply-to: shavitt@mps.ohio-state.edu To originators and distributors of quantum chemistry ab initio programs: At the invitation of the Annual Review of Physical Chemistry, we have been writing a survey of ab initio quantum chemistry programs. The survey is limited to ab initio programs, and is expected to cover only widely distributed packages, including programs distributed free and those sold commercially, but will not cover programs used mostly by their originators and their friends. The survey will not try to compare the speed at which different programs run, because such comparisons are strongly affected by the choice of problems and computer systems. Instead, it will focus on the capabilities of the different packages and their distinctive features. As input for that survey, we are asking originators and distributors of ab initio quantum chemistry packages to respond to the following questionaire about their packages. The responses will help ensure the accuracy of the information about each package that will appear in the survey. Your answers need not be limited to short responses to the questions asked. You may elaborate upon your answer or, if the question is not relevant or not framed appropriately for the context of your programs, you may ignore it or provide the relevant information in an alternative form. Even a partial response will be better than no response at all. Your help will be acknowledged in the published survey. Please send your response by e-mail to shavitt@mps.ohio-state.edu or by mail or fax to I. Shavitt at the address listed at the end of this message. A very early response will be greatly appreciated and will help us meet the submission deadline. QUESTIONAIRE ABOUT AB INITIO QUANTUN CHEMISTRY PROGRAMS 0. NAME 0.1. Please provide the name (and version, if appropriate) of your package. 0.2. Name of the respondent to this questionaire (with address, e-mail address, and telephone number, please). 1. BASIS SETS 1.1. What types of basis sets can your program use? (STO, GTO, CGTO = contracted GTO, etc.) 1.2. If CGTO, does it handle general contractions (without having to repeat shared primitives)? 1.3. If GTO/CGTO, does it use Cartesian Gaussians, spherical harmonic Gaussians (in real form), or both (or arbitrary linear combinations of Cartesian Gaussians)? (This question pertains, e.g., to the ability to use 5 or 6 components for d functions, 7 or 10 for f, etc.) 1.4. What is the limit, if any, on the l-values of your basis functions (d, f, g, etc.)? 1.5. Are collections of basis sets included in the program, and can the user add to these collections? 1.6. Are there other specific or distinctive features about basis set capabilities in your programs? 1.7. Are there specific limits (independent of a particular computer's capacity) on the number of basis functions, the number of primitives per CGTO, total number of primitives, etc.? 2. INTEGRALS CALCULATION 2.1. Does your package have its own original integrals program, or does it use an independently developed program, and if the latter, what is its name (and version, if appropriate)? 2.2. Please identify the computational algorithm(s) used in the integrals program (e.g., McMurchie-Davidson, PRISM, etc.). 2.3. Does your integrals program take advantage of spatial symmetry, and if so, by what mechanism and for which point groups? 2.4. Are the integrals provided over atomic basis functions or over symmetry-adapted combinations of atomic basis functions? 2.5. In what forms can the geometry data be provided to the program (Cartesian coordinates, Z-matrix, etc.)? 2.6. Can effective core potentials be used, including relativistic effective core potentials? 2.7. What is the format of the integrals file (labeled lists, supermatrix)? 2.8. To what extent can integrals be reused? 2.9. Are there any distinctive features or limitations for integrals calculation in your program? 3. WAVE FUNCTION MODELS 3.1. Self-Consistent Field (Hartree-Fock) capabilities: 3.1.1. Which SCF (HF) models are implemented (RHF, UHF, ROHF, etc.)? 3.1.2. In ROHF, what types of open-shell configurations can be handled? 3.1.3. Does the SCF program take advantage of symmetry, and if so, for which point groups? 3.1.4. Which convergence-acceleration methods are provided (DIIS etc.)? 3.1.5. Can user-supplied starting guesses be used? 3.1.6. Can the SCF calculations be restarted? 3.1.7. Are there "direct SCF" capabilities? 3.1.8. Can the SCF solution be tested for stability? 3.1.9. Are there specific limits (independent of a particular computer's capacity) on the size of the molecules or basis sets that can be handled? 3.1.10. Are there other specific or distinctive features about SCF capabilities in your programs? 3.2. Multiconfigurational SCF capabilities: 3.2.1. Which, if any, MCSCF models are implemented (CASSCF only, or more general choices of configuration)? 3.2.2. Does the MCSCF program take advantage of symmetry, and if so, for which point groups? 3.2.3. Which method(s) are used for MCSCF wave function optimization? 3.2.4. Can user-supplied starting guesses be used? 3.2.5. Can MCSCF calculations be restarted? 3.2.6. Are there specific limits (independent of a particular computer's capacity) on the number of configuration state functions or occupied orbitals in your MCSCF program? 3.2.7. Are there other specific or distinctive features of the MCSCF capabilities in your program? 3.3. Configuration interaction capabilities: 3.3.1. Which, if any, CI models are implemented? This covers levels of excitation (CISD, etc.), reference space (single- or multireference), orbital basis (RHF, UHF), or other relevant features, such as internal contraction. 3.3.2. In the multireference case, are there limitations on the choice of the reference configurations (e.g., arbitrary, or restricrted to an "active space" or to CAS)? 3.3.3. Is the CI expansion in terms of determinants, spin-adapted configurations, spin-and-symmetry-adapted configurations (configuration state functions, CSF), or other? 3.3.4. If spin-adapted configurations are used, what is the spin-coupling mechanism (projection operators, bonded functions, symmetric group, unitary group, etc.)? 3.3.5. If the configurations are symmetry-adapted, which point groups can be treated? 3.3.6. Can user-supplied starting guesses be used? 3.3.7. Can CI calculations be restarted? 3.3.8. Which size-consistency corrections (Davidson, Pople, etc.), if any, are available? 3.3.9. What is the basic method used in the CI program (many-body formalism, Slater-Condon rules, unitary group, etc.)? 3.3.10. Is the approach "direct CI", "conventional CI", or either? 3.3.11. Please describe configuration selection capabilities, if any. 3.3.12. Are there specific limits (independent of a particular computer's capacity) on the on the size of the CI calculations (number of reference configurations, total number of configurations, number of active orbitals, etc.)? 3.3.13. Are there other specific or distinctive features of the CI capabilities in your program? 3.4. Single-reference perturbation-theory methods: 3.4.1. Which types of perturbation-theory calculations (Rayleigh- Schroedinger, Brillouin-Wigner, etc.), if any, are implemented? 3.4.2. Which orbital partitionings (Moller-Plesset, Epstein-Nesbet, etc.) are available? 3.4.3. What is the implementation method (many-body, configuration- based)? 3.4.4. Which types of reference function and orbital bases (RHF, UHF, ROHF, arbitrary, etc.) can be used? 3.4.5. Which orders of PT are implemented for each of the available models? 3.4.6. Is spatial symmetry utilized for each of the orders and models, and for which point groups? 3.4.7. Is "direct" calculation (without integrals storage) available for MP2 or any other MBPT model? 3.4.8. Are there other specific or distinctive features of the PT capabilities in your program? 3.5. Single-reference coupled-cluster method: 3.5.1. Which coupled-cluster models (CCD, CCSD, QCISD, CCSD(T), etc.), if any, are implemented? 3.5.2. Which types of reference function and orbital bases (RHF, UHF, ROHF, etc.) can be used for each of the available models? 3.5.3. Is spatial symmetry utilized for each of the available models? 3.5.4. Are there other specific or distinctive features of the CC capabilities in your program? 3.6. Multireference methods: 3.6.1. Are there any multireference PT or CC models available in your programs? 3.6.2. If yes, please provide a brief description and/or references for these models. 3.7. Coupled-pair approximations: 3.7.1. Which coupled-pair approximations (CEPA, CPF, ACPF, linearized CC, etc.), if any, are available in your programs? 3.7.2. Which of the available methods can be used in a multireference context? 3.7.3. Are there any specific aspects or distinctive features of the coupled-pair approximations in your programs? 3.8. Other models: 3.8.1. Are there any other wave function models, such as valence-bond, GVB, equations-of-motion, implemented in your programs? 3.8.2. If yes, please provide a brief description and/or references. 4. DERIVATIVES, GEOMETRY OPTIMIZATION AND VIBRATIONAL FREQUENCIES 4.1. Please specify the level of analytical energy derivatives (gradients, Hessians, etc.) available for each model in your programs. 4.2. To what extent is symmetry utilized in the calculation of the analytical energy derivatives in each case? 4.3. For which models, if any, is automatic geometry optimization available in your programs, and which level of analytical derivatives is used in each case? 4.4. Can transition states be optimized, at which level, and by which approach? 4.5. Can selected geometry parameters be frozen in geometry optimization? 4.6. For which models, if any, is automatic calculation of harmonic vibrational frequencies available in your programs, and which level of analytical derivatives is used in each case? 4.7. Does the program provide a description of the normal coordinates? 4.8. Can anharmonic vibrational frequencies be obtained? 4.9. To what extent can symmetry be used in geometry optimization and frequency calculation in each model? 4.10. What are the restart capabilities in geometry optimization and frequency calculation? 4.11. Are there any important limitations on analytical derivatives calculation, geometry optimization, and frequency calculation in your programs? 4.12. For which models can IR and/or Raman intensities be computed? 4.13. Are there other specific or distinctive features relating to energy derivatives, geometry optimization, and vibrational frequencies in your programs? 5. OTHER PROPERTIES 5.1. Which first-order electronic properties (operator expectation values), if any, are available for each model in your programs? 5.2. Which second-order electronic properties, if any, are available for each level in your program? 5.3. If second-order properties are available, are they calculated by finite differences, analytical derivatives, or perturbation series? 5.4. Please describe any facilities for the treatment of relativistic effects, including spin-dependent operators, and/or relativisitic calculations. 5.5. Are there other specific or distinctive features relating to properties calculation in your programs? 6. OTHER CAPABILITIES 6.1. Please describe briefly any other capabilities or distinctive features (e.g., solvation) in your programs (please provide references, if appropriate). 7. HISTORY AND REFERENCES 7.1. A short history of the origin and evolution of your programs (with, or in the form of, a list of references) would be appreciated. The references requested here are specifically to the programs, rather than the methods; references to methods are requested in Question 7.3. 7.2. What is the proper citation of your programs in the literature (i.e., a reference to be cited by a user in a publication based on the programs)? (A citation for the latest version would be sufficient.) 7.3. A list of your favorite references for the methods used in your programs whould be helpful. 7.4. If you wish, you may provide here selected references to applications which illustrate the capabilities and performance of your programs. 7.5. Can you provide any information on the extent of the distribution and use of your programs? 8. AVAILABILITY 8.1. How can a potential user obtain your programs (from a program exchange, such as QCPE or CPC, direct from the authors, by ftp, or other means)? Please provide program number, if applicable, appropriate mail or e-mail addresses, phone numbers, etc. 8.2. Is there a payment for the programs, and if so, is it primarily to cover the cost of providing the copy, etc., or are commercial fees charged? 8.3. In what form is the documentation provided (on line, manual, etc.)? 8.4. What help facilities, if any, are available? 8.5. Which computers/operating systems can run your programs? 8.6. Do you provide the source code? 8.7. Which programming languages (Fortran, C, assembler) are used? 8.8. Can a potential user easily port the programs to a different computer/operating system? 8.9. Are parallel versions of your programs available or under development, for which machines, and using which approach (message passing, parallel Fortran extensions, etc)? 8.10. Are there graphical interfaces or other user interfaces available for user interaction with the programs, including input preparation and/or output analysis? 8.11. Are there other aspects of the availability and porting of the programs that you would like to describe? 9. OTHER 9.1. Is there any other information or comments you would like to provide? -----------------------End of Questionaire ------------------------ Thank you very much for your participation. Isaiah Shavitt, Department of Chemistry, Ohio State University, Columbus, OH 43210-1173 e-mail: shavitt@mps.ohio-state.edu Phone: 614-292-1668 Fax: 614-292-1685 Janet Del Bene, Department of Chemistry, Youngstown State University, Youngstown, OH 44555 e-mail: fr042008@ysub.bitnet Phone: 216-742-3466 Fax: 216-742-1579 Jan K. Labanowski, Ohio Supercomputer Center, 1224 Kinnear Road, Columbus, OH 43212-1163 e-mail: jkl@ccl.net Phone: 614-292-9279 From ross@cgl.ucsf.EDU Tue Dec 21 21:19:30 1993 Received: from socrates.ucsf.EDU for ross@cgl.ucsf.EDU by www.ccl.net (8.6.4/930601.1506) id VAA12571; Tue, 21 Dec 1993 21:08:56 -0500 Received: from localhost by socrates.ucsf.EDU (8.6.4/GSC4.24) id SAA27706; Tue, 21 Dec 1993 18:08:55 -0800 Date: Tue, 21 Dec 1993 18:08:55 -0800 Message-Id: <199312220208.SAA27706@socrates.ucsf.EDU> From: ross@cgl.ucsf.edu (Bill Ross ) To: chemistry@ccl.net, mailh@comp.bioz.unibas.ch Subject: Re: L-J parameters for Calcium ion >I am trying to do some MD simulations involved Calcium ions, but I cannot >find the parameters (sigma and epsiron) of the LJ potential for the ion. > Check out: L.J. Bartolotti, L.G. Pedersen & P.S. Charifson, "Long Range > Nonbonded Attractive Constants for Some Charged Atoms", J. Comp. Chem., > Vol. 12, No. 9, 1125-1128 (1991). > These parameters work well in simulations (claims based on FEP calculations > of hydration free energies). For calcium it gives C6 = 2.58 kcal A^6/mol > and C12 = 35.8 kcal A^12/mol. The paper gives C6 parameters for other metal > ions (Li, Na,K,Rb, Cs, Be, Mg, Sr, Ba, Al, Sc, Cr, Mn, Fe, Cu, Zn, Ga, Ge, > Se, Ru, Ag, Cd, In, Sn, Eu), too, but not always C12 parameters. However, > the authors present a simple scheme to calculate C12 parameters from the > corresponding C6 parameters. A word of warning for those converting the A,B form parameters to r*,eps: The simple translation formulas one can derive to map A,B to r*,epsilon set the potential to be the same between atoms of the given type under both conventions. BUT, note that owing to the different combining rules associated with these two forms of notation, the per-atom potentials derived this way result in different distances of the minimum for pairs of atoms of _different_ types (the depth of the potential is also different but is much less sensitive to the combining rules). Thus it was necessary to derive the r* values for the Aqvist monovalent cations to reproduce the ion-OH2 potential in the A,B scheme (rather than the ion-ion potential) in order to get the correct free energies of solvation in water (Bayly & Miyamoto, unpublished results). Insofar as ions are more likely to contact oppositely charged atoms than each other, it makes more sense to translate the parameters with this in mind; partially charged atom types of which all instantiations have charges of predictable sign may also be worth considering in this light. Bill Ross