From states@ibc.wustl.edu Thu Jun 30 11:04:28 1994 Received: from wugate.wustl.edu for states@ibc.wustl.edu by www.ccl.net (8.6.9/930601.1506) id KAA23022; Thu, 30 Jun 1994 10:45:39 -0400 Received: by wugate.wustl.edu (5.67b/WUSTL-0.3) with SMTP id AA28747; Thu, 30 Jun 1994 09:45:38 -0500 Received: by ibc.WUStL.EDU (5.0/SMI-SVR4) id AA13728; Thu, 30 Jun 1994 09:45:37 +0600 Date: Thu, 30 Jun 1994 09:45:37 +0600 From: states@ibc.wustl.edu (David J. States) Message-Id: <9406301445.AA13728@ibc.WUStL.EDU> To: h.rzepa@ic.ac.uk, chemistry@ccl.net Subject: Re: CCL:Chemical MIME types X-Sun-Charset: US-ASCII Content-Length: 1998 There is a real need for a chemical MIME type. Molecules are a very basic elements of reality, and chemists have developed an extensive formalism to describe them. Being able to exchange basic chemical information between applicatons would be extremely useful. The chemical community also needs better agreement on standards. You can download a .gif file and expect to view it. Transfering a coordinate set from one application to another is much a more speculative proposition. FASTA format macromolecular sequence data should be a secondary MIME type. Even though it is ambiguous (you can only statistically guess whether the data is a nucleic acid (4 letter alphabet) or a protein (20 letters)), FASTA is the most widely supported sequence format in use. There should also be an additional protein sequence secondary type, either SwissProt or PIR (or both). The GCG format is proprietary and not supported by all packages, and the NSBI/ASN format is very complex and also not widely supported outside of NCBI software. How much of the NCBI/ASN.1 definitions are you proposing to include? The chemical definitions are embedded in a much broader definition set encompassing everything from bibliographic citations to the syntax for defining a gene. Because the definitions are highly cross-referenced, teasing out just chemistry would be difficult. Should a CAS registry number be a MIME type? I guess I raise it to oppose it. They really do not communicate the data, only a pointer to it, and the registry numbers have been closely protected by CAS. For example, I don't think CAS would allow a general RN <-> SMILES string table to be distributed freely. If they did, I would reconsider. Do I hear anyone volunteering to maintain a general secondary MIME type coercion filter so that users need only have a limited number of viewers on their system and programmers could limit their target? David States Institute for Biomedical Computing / Washington University in St. Louis From aiba@debye.vmsmail.ethz.ch Thu Jun 30 12:04:27 1994 Received: from bernina.ethz.ch for aiba@debye.vmsmail.ethz.ch by www.ccl.net (8.6.9/930601.1506) id LAA23473; Thu, 30 Jun 1994 11:16:48 -0400 Message-Id: <199406301516.LAA23473@www.ccl.net> Received: from DEBYE.vmsmail.ethz.ch by bernina.ethz.ch id <10338-0@bernina.ethz.ch>; Thu, 30 Jun 1994 17:16:37 +0200 X-Vms-To: ETHZ::"chemistry@ccl.net" To: chemistry@ccl.net From: aiba@debye.vmsmail.ethz.ch (Aiaz Bakassov, Phys. Chem., ETH Zurich) Subject: G92. QUE. Batch job termination control. Date: Thu, 30 Jun 1994 17:16:37 +0200 Dear netters, I run G92 in batch mode, both in VMS and in UNIX. I wait for G92 normal termination and then I interface the output of G92 to some "my_code". Then I routinely change parameters in the input file for G92 and again submit it to batch queue, and again wait for completion and again run "my_code". It's a loop, isn' it ? But the problem is how to tell the system (VMS or/and UNIX) whether the G92 batch job has already terminated, so to allow the system (VMS or/and UNIX) to execute "my_code" which uses G92 output. It must be some command in a VMS .com file or in a UNIX shell which waits for G92 to terminate. Otherwise, the execution of "my_code" is meaningless. I believe it's a standard situation to many other standard routines too (not only G92) and the best solutions (to VMS and to UNIX separately) are well known. Does anybody advise us on this ? Are there good references (VMS/UNIX books) where the solutions are being discussed ? I would prefer purely OS (operating system) solution, for I already know that one can write FORTRAN code in VMS using lib$spawn function. That seems very awkward to me (to go from FORTRAN to VMS and back several times within one program) No similar thing is known to me for UNIX. But that seems awkward I repeat myself. Sincerely, ---------------------------------------------------------------------- Aiaz BAKASSOV (English: Ayaz BAKASOV) | Phone: +41 1 632 79 18 Laboratorium fuer Phys. Chemie | FAX: +41 1 632 10 21 ETH-Zuerich (Zentrum) | E-mail: aiba@debye.vmsmail.ethz.ch CH-8092 Zurich, Switzerland | aiba@ir.lpc.ethz.ch ---------------------------------------------------------------------- From setlik@acsu.buffalo.edu Thu Jun 30 14:04:28 1994 Received: from lictor.acsu.buffalo.edu for setlik@acsu.buffalo.edu by www.ccl.net (8.6.9/930601.1506) id NAA25323; Thu, 30 Jun 1994 13:24:19 -0400 Received: (setlik@localhost) by lictor.acsu.buffalo.edu (8.6.8/8.6.4) id NAA08394 for CHEMISTRY@ccl.net; Thu, 30 Jun 1994 13:23:59 -0400 Date: Thu, 30 Jun 1994 13:23:59 -0400 From: "Robert F. Setlik" Message-Id: <199406301723.NAA08394@lictor.acsu.buffalo.edu> To: CHEMISTRY@ccl.net Subject: ques on mol dynamics Dear netters, Does anyone know of molecular dynamic simulations on metalloproteins? I am looking for work done on proteins with active sites similar to that of alkaline phosphatase. Also any information on work done on MG++ complexes would be helpful. Cheers, Rob Setlik Dept of Biophysics Roswell Park Cancer Inst. Elm and Carlton Streets Buffalo, N.Y. 14263 From axh14@cac.psu.edu Thu Jun 30 14:06:06 1994 Received: from milkman.cac.psu.edu for axh14@cac.psu.edu by www.ccl.net (8.6.9/930601.1506) id NAA25341; Thu, 30 Jun 1994 13:27:43 -0400 Received: from wilbur.cac.psu.edu by milkman.cac.psu.edu with SMTP id AA27553 (5.65c/IDA-1.4.4 for ); Thu, 30 Jun 1994 13:27:39 -0400 From: ARTHUR HOAG Received: by wilbur.cac.psu.edu id ; Thu, 30 Jun 1994 13:27:38 -0400 Date: Thu, 30 Jun 1994 13:27:38 -0400 Message-Id: <199406301727.AA19091@wilbur.cac.psu.edu> To: chemistry@ccl.net Subject: G92:MP4 Restarts I have been having trouble restarting my MP4 jobs on the PSC c90. I use "# opt=restart MP4 6-31G(d) scf=restart optcyc=20" I usually use this line because my jobs get terminated for system maintenance, so i need to restart scf as well. but, if i get through the 5th fletcher-powell cycle, it terminates because this is the default maxcycles (I assume). So according to the manual I restart with optcycle set higher than five, since the cycle count does not reset. BUT, this doesn't seem to work. My jobs quit after the first restart cycle saying that cycle 5 is done..... HELP???? thanks in advance Arthur Hoag axh14@wilbur.cac.psu.edu ph 814-863-7980 From cletner@remcure.bmb.wright.edu Thu Jun 30 16:04:30 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id PAA27408; Thu, 30 Jun 1994 15:26:06 -0400 Received: by remcure.bmb.wright.edu (920330.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA03676; Thu, 30 Jun 94 15:15:23 -0700 Date: Thu, 30 Jun 1994 15:14:31 -0700 (PDT) From: Charles Letner Subject: Imaging program To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello all, I have an 2D array of numbers between 0 and 255 that has been produced from a NMR data set. I would like to put these into a grey scale image with 256 shades of grey and then output to any common graphics format, ie/ tiff, bmp, etc... Does anyone know of a program/utility that can accomplish this? The array has been created with a C program so it would be fairly easy to change the array so that it is compatable with the image creation program/utility. Any leads will be greatly appreciated. Best regards, Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From KZHANG@MIAMIU.ACS.MUOHIO.EDU Thu Jun 30 18:04:31 1994 Received: from MIAMIU.ACS.MUOHIO.EDU for KZHANG@MIAMIU.ACS.MUOHIO.EDU by www.ccl.net (8.6.9/930601.1506) id RAA29560; Thu, 30 Jun 1994 17:52:27 -0400 Message-Id: <199406302152.RAA29560@www.ccl.net> Received: from MIAMIU by MIAMIU.ACS.MUOHIO.EDU (IBM VM SMTP V2R2) with BSMTP id 8917; Thu, 30 Jun 94 17:52:39 EST Received: from MIAMIU (KZHANG) by MIAMIU (Mailer R2.08) with BSMTP id 4291; Thu, 30 Jun 94 17:52:38 EST Date: Thu, 30 Jun 94 17:42:30 EST From: Kui Zhang Subject: Ques on calculations of La's and Ac's elements To: chemistry@ccl.net Does anyone know of methods which are able to treat Lanthanide and Actinide elements. I want to calculate a bunch of molecules containing these elements using either ab initio or semiempirical method. Any information and suggestion would greatly appreciate. Kui Zhang e-mail: kzhang@miamiu.acs.muohio.edu From CUNDARIT@MSUVX1.MEMPHIS.EDU Thu Jun 30 19:04:35 1994 Received: from msuvx1.memphis.edu for CUNDARIT@MSUVX1.MEMPHIS.EDU by www.ccl.net (8.6.9/930601.1506) id SAA29833; Thu, 30 Jun 1994 18:52:56 -0400 From: Received: from MSUVX1.MEMPHIS.EDU by MSUVX1.MEMPHIS.EDU (PMDF V4.3-8 #5958) id <01HE5TNTA1HGA3HZXN@MSUVX1.MEMPHIS.EDU>; Thu, 30 Jun 1994 17:52:39 -0500 (CDT) Date: Thu, 30 Jun 1994 17:52:39 -0500 (CDT) Subject: Re: CCL:Ques on calculations of La's and Ac's elements To: KZHANG@MIAMIU.ACS.MUOHIO.EDU Cc: chemistry@ccl.net Message-id: <01HE5TNTA1HIA3HZXN@MSUVX1.MEMPHIS.EDU> X-VMS-To: IN%"KZHANG@MIAMIU.ACS.MUOHIO.EDU" X-VMS-Cc: IN%"chemistry@ccl.net" MIME-version: 1.0 Content-type: TEXT/PLAIN; CHARSET=US-ASCII Content-transfer-encoding: 7BIT >Does anyone know of methods which are able to treat Lanthanide and >Actinide elements. I want to calculate a bunch of molecules containing >these elements using either ab initio or semiempirical method. Any >information and suggestion would greatly appreciate. > >Kui Zhang Howdy, Our group in collaboration with Walt Stevens developed an ECP scheme for the lanthanides that is consistent with those developed by Walt et al. for the TMs. The ref. is J Chem Phys, 1993, 98, 5555. Dolg and associates have developed ECPs for the lanthanides (Theor Chim Acta 1989, 75, 369 and J Chem Phys 1989, 90, 1730 are the refs, I believe). Ross et al. have a lanthanide ECP scheme, but I do not know if that has been published yet. The Dolg group has used their Ln's and as I recall seen good agreement between calcd and exptl energetic data. We have just finished testing our Ln ECPs out for prediction of the geometries of the 56 LnX3 compounds (Ln = Ce to Lu; X = F, Cl, Br, I) and see agreement with electron diffraction data to within 2% for the Ln-X bond lengths. Off the top of my head, I can't recall ever seeing all-electron calcs on lanthanide complexes. Pyykko may have done some relativistic, one-center expansion (OCE) calcs on lanthanide hydrides. The exact ref should be in his recent Chem Rev paper on relativistic effects in chemistry. Zerner and co-workers have performed INDO calcs on lanthanide complexes. The ref is Theor Chim Acta 1987, 71, 21 and there is a more recent one which I believe is in TCA. Jing-Qing et al. have done some INDO calcs. on Ln organometallics. One ref I have is Int. J. Quantum Chem 1986, 29, 1017. As for actinide calcs the best source is the recent Chem Rev article by Bursten. It has appeared within the past three years or so. Jeff Hay has also done some ECP calcs for An(CH3)3 complexes, this was a JACS communication with Ortiz and Martin. Sorry no ref, it's at home! Hope this helps. Let me know if there are more Ln calcs out there! Tom ------------------------------------------------------------------------------ Thomas R. Cundari Address until the end of August Asst. Professor of Chemistry Tom Cundari Computational Inorganic Chemistry Lab Visiting Scientist University of Memphis CST-3, C346 Memphis, TN 38152 Los Alamos National Lab phone: 901-678-2629 Los Alamos, NM 87545 fax: 901-678-3447 e-mail: cundarit@memstvx1.memst.edu http://www.memst.edu/chemistry/umchem.html ------------------------------------------------------------------------------- From Patrick.Bultinck@rug.ac.be Thu Jun 30 10:31:21 1994 Received: for chemistry-request@ccl.net by www.ccl.net (8.6.9/930601.1506) id FAA19253; Thu, 30 Jun 1994 05:04:48 -0400 Received: from mserv.rug.ac.be for Patrick.Bultinck@rug.ac.be by www.ccl.net (8.6.9/930601.1506) id EAA19023; Thu, 30 Jun 1994 04:37:59 -0400 Received: from allserv.rug.ac.be by mserv.rug.ac.be with SMTP id AA24850 (5.67b/IDA-1.5 for ); Thu, 30 Jun 1994 10:37:16 +0200 Received: by allserv.rug.ac.be (5.0/SMI-SVR4) id AA27075; Thu, 30 Jun 94 10:34:10 +0200 Date: Thu, 30 Jun 1994 10:34:09 +0200 (MET DST) From: Patrick Bultinck Subject: CCL:SUMMARY:elec.pot.:basisset depend. To: chemistry@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Content-Length: 11141 Sender: chemistry-request@ccl.net Errors-To: ccl@ccl.net Precedence: bulk Netters, Please hereby find a summary of the answers C I received on the basis set dependancy of the charges fitted to the electrostatic potential, and the electrostatic potential itself. Hereby I wish to thank everybody who shared experiences, references, opinions, and such... ORIGINAL MESSAGE Hello netters, Does anybody have a reference, or rather an opinion or experience with the basisset dependance of the electrostatic potential. I would like to fit the charges to this potential since the n-dep. in S^nPS^(1-n) in Mulliken (n=0) and Lowdin PA (n=0.5) scares me off a little. That is why I would like to know how the basis set dep. of the elect. pot. behaves compared with the MPA and LPA approaches... Any comments much appreciated, (let me know if interested in a summary) Patrick, University of Ghent, Belgium, Patrick.Bultinck@rug.ac.be AND HERE ARE THE ANSWERS Patrick: I have done quite a few fits of partial atomic charges to the electrostatic potential using the CHELPG program as coded in G92. In my experience, once you are using fairly large basis sets, the magnitudes of the partial charges decrease regularly as the size of the basis set increases, both at the HF and MP2 levels of calculation. On the other hand, the Mulliken-derived charges tend to increase (but less uniformly) in magnitude as basis set size increases. For example, for oxygen in Si(OH)4 at the HF level: 6-311G** basis 6-311G(2d,2p) basis Mulliken CHELPG Mulliken CHELPG - -0.711 -0.935 -0.881 -0.858 This trend is fairly typical of what I have seen. I don't know how large a basis would be required to get convergence of this charge? Hope this is in some way useful. Good luck. Brian Teppen teppen@soilchem.uark.edu Partrick, This is a very interesting question that you have asked, and I would be interested in seeing a summary of the reponses that you recieve. You might be interested in two references that I happen to have had laying on my desk.... Jug, K. Theoret. Chim. Acta 39,301-312 (1975) Jug, K. Theoret. Chim. Acta 31, 63-73 (1973) These papers actually pertain more to charge distributions but there are discussions (particularly in the first reference) to the influence of basis sets on the calculation of electronic properties (multipole moments). Thanks in advance for the summary and I hope this was somewhat helpful. Kris Kristopher Wise Dept. of Chemistry and Biochemistry University of Oklahoma KEWISE@aardvark.ucs.uoknor.edu You might find useful to have a look to J.Comp.Chem., 11, 416 (1990) JACS, 113, 5203 (1991). and references therein Good luck! M. Orozco Patrick, You might find some information from F.J.Luque, F.Illas and M.Orozco, J.Comp.Chem., 11(1990)416; G.P.Ford and B. Wang, J.Comp.Chem., 14(1993)1101, 15(1994)200. Roughly, Large basis sets generate a flat MEP with shallow wells but large mep charges; minimal basis set gives a MEP with deeper wells, smaller values in the far region and, therefore, smaller mep charges. Have a nice day, Bingze Wang IRBM, Rome, wang@irbm.it Hello Patrick, I've just published a paper about the basis set dependence of ESP charges in a several set dependence of ESP charges in a several molecules. The dependence is much better than the dependence of Mulliken charges. It is much more convergent as the basis set was increased. The paper will appear in JCC in aug or sept 94. Now I am about to leave for holydays so if you are interested in more detail be fast. - ---------------------------------------------------------- Gabor I. Csonka Budapest University of Technology Tel/FAX: (361) 18.12.177 Inorganic Chemistry Dept. Ch. Bldg csonka@iris.inc.bme.hu H-1111, Bp. Szent Gellert ter 4 - ---------------------------------------------------------- If it is true that the electron distribution is basis set-dependent, it would follow that the ESP will be basis set-dependent. Much work has gone into the plotting of electron density maps and density difference maps (The work of R. F. Bader is a good starting point.). These maps clearly show basis-set dependence, rather dramatically for di- and tri-atomics. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ FREDERIC A. VAN-CATLEDGE Scientific Computing Division || Office: (302) 695-1187 or 529-2076 Central Research & Development Dept. || The DuPont Company || FAX: (302) 695-9658 P. O. Box 80320 || Wilmington DE 19880-0320 || Internet: fredvc@esvax.dnet.dupont.com - -------------------------------------------------------------------------------- Opinions expressed in this electronic message should ***> NOT <*** be taken to represent the official position(s) of the DuPont Company. *****> ANY OPINIONS EXPRESSED ARE THE PERSONAL VIEWS OF THE AUTHOR ONLY. <***** ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Dear Computational Chemist: 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 needed. Reliable net atomic charges can be found by fitting the molecular electric potential with program PDM93. In addition to net atomic charges, program PDM93 also allows any combination of atomic dipoles/quadrupoles, bond dipoles, as well as the addition of lone pair electron sites if required. A particularly useful feature of the program is the transparent way in which fixed charges and charge dependency conditions are specified. By specififying 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. I append a brief description of program PDM93. -Don Williams Program PDM93, Potential Derived Multipoles The following is a brief description of this program. Molecules interact with each other via their electric potential. PDM93 finds optimized net atomic charges and other site multipole representations of the molecular electric potential based on a variety of models. The program is easy to use, flexible and powerful. Results are obtained in a single iteration and a complete error treatment is made which includes estimated standard deviation and correlation of variables. The program is written in Fortran 77 and runs on Unix, Vax, and other computers with F77 capability. Program PDM93 has a unique combination of features: o general sites, e.g. united atoms, not necessarily at atomic locations o each site may have any combination of monopole, dipole, or quadrupole o bond dipole model is supported o restricted (along the bond direction) bond dipole model is supported o provision for site dipole vectors in sp2 or sp3 directions o selected fixed atomic charges o selected groups of atoms with fixed charge o atomic charge equalities or symmetry relations o rotational invariance of site charges o provision for optional foreshortening of X-H bonds o comparison with Mulliken charges and Mulliken electric potential o direct input from Gaussian-92 output file o generalized input from other quantum mechanics programs o automatic generation of electric potential grid points o provision for custom generation of grid points o on-line program manual o comprehensive examples are provided A review of potential-derived charges may be found in Reviews of Computational Chemistry, Vol. II, pp. 219-271 (1991). For further information contact Dr. Donald E. Williams, Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA. Tel:(502)852-5975 Fax:(502)852-8149 E-mail:dew01@xray5.chem.louisville.edu - ----------------------------------------------------------------------- Ordering information Program package consisting of manuals, Fortran-77 source files, and demonstration example files.........price reduced!.............$1,600 Discount price for academic institutions only........................$395 Choose the preferred method of shipment: Via ftp, purchaser furnishes valid ftp address*...............n/c *account must be password-protected; please provide a temporary password for delivery Via magnetic media DC6150 tape cartridge.................................$20 MP120 tape cartridge, unix tar format..................$5 or MP120 tape cartridge, Vax backup format................$5 Make check payable to the University of Louisville. - ------------------------------------------------------------------------- Patrick, > > Does anybody have a reference, or rather an opinion or experience with > the basisset dependance of the electrostatic potential. > This has been studied extensively. See: Rodriguez et al. J. Comp. Chem. 14 (1993) 922. Alkorta et al. J. Comp. Chem. 14 (1993) 530. Alema'n et al. J. Comp. Chem. 14 (1993) 799. Earlier work is referenced therein. CJC - -- Christopher J. Cramer University of Minnesota Department of Chemistry 207 Pleasant St. SE Minneapolis, MN 55455-0431 (612) 624-0859 cramer@maroon.tc.umn.edu Hi Patrick, > > the basisset dependance of the electrostatic potential. > > I would like to fit the charges to this potential since the n-dep. in > S^nPS^(1-n) in Mulliken (n=0) and Lowdin PA (n=0.5) scares me off a little. > That is why I would like to know how the basis set dep. of the elect. pot. > behaves compared with the MPA and LPA approaches... > I've used CHELPG charges (G92, POP=(CHELPG,DIPOLE) and available in GAMESS as well) for a few projects as have others in my group. I calculate a couple of basis sets for comparison and have seen changes, but only on a small scale (<0.07 e) as long as at least 6-31G(d) was used for the basis set. Correlation seems to cause more changes (understandably), but the variations are no where near what you see with Mulliken. I've had Mulliken charges which yield a dipole moment which is off by 1.2D! CHELPG gets the dipole moment almost right even when you don't constrain it. Dan Once such reference is: Truhlar et al. in "Chemical Applications of Atomic and Molecular Potentials", Politzer and Truhlar, eds. Plenum Press, NY 1981. It's old but still should be useful. For basis set comparison of fits to electrostatic potentials, see J.Comp. Chem. 8, 894 (1987). Michelle M. Francl Associate Professor of Chemistry Bryn Mawr College Bryn Mawr, PA 19010 Phone: 610-526-5108 FAX: 610-526-5086 Internet: mfrancl@cc.brynmawr.edu Hi there, I just came across your mail in CCL, and was wondering if you know of any programs (public domain, or free) that would fit charges to the electrostatic potential. I am in a need for such a program. Thanks for any help that you might have to offer. regards, sundar email sveliah@fsh.mtu.edu