From hughc@extro.ucc.su.oz.au Thu Nov 3 00:23:19 1994 Received: from extra.ucc.su.OZ.AU for hughc@extro.ucc.su.oz.au by www.ccl.net (8.6.9/930601.1506) id XAA24078; Wed, 2 Nov 1994 23:28:41 -0500 Received: from hugh (hugh.pharmacol.su.OZ.AU [129.78.41.50]) by extra.ucc.su.OZ.AU (8.6.8.1/8.6.9) with SMTP id PAA19631 for ; Thu, 3 Nov 1994 15:28:25 +1100 Message-Id: <199411030428.PAA19631@extra.ucc.su.OZ.AU> X-Sender: hughc@postbox.su.edu.au Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 03 Nov 1994 15:27:56 +1000 To: chemistry@ccl.net From: hughc@extro.ucc.su.OZ.AU (Hugh Capper) Subject: Amber X-Mailer: Dear CCLers, I am looking for a version of AMBER to run on a SGI or Intel X86 or the source code to compile it for the above can anybody help me? Thanks in advance, Hugh Capper Dept of Pharmacology The Uni. of Sydney From toukie@zui.unizh.ch Thu Nov 3 06:23:24 1994 Received: from rzusuntk.unizh.ch for toukie@zui.unizh.ch by www.ccl.net (8.6.9/930601.1506) id FAA26655; Thu, 3 Nov 1994 05:33:14 -0500 Received: by rzusuntk.unizh.ch (4.1/SMI-4.1.9) id AA25869; Thu, 3 Nov 94 11:33:11 +0100 X-Nupop-Charset: British Date: Thu, 3 Nov 1994 11:27:30 +0100 (MET) From: "Hr Dr. S. Shapiro" Sender: toukie@zui.unizh.ch Reply-To: toukie@zui.unizh.ch Message-Id: <41250.toukie@zui.unizh.ch> To: chemistry@ccl.net Subject: Rate of rotation of methyl groups Dear Colleagues: I am seeking information on the rate of rotation of methyl groups: (i) firstly, I am seeking information/references describing the rate of rotation of the terminal methyl groups of n-alkanes at ca. room temperature (either experimental or theoretical). (ii) secondly, I am seeking information/references describing the rate of rotation of the C-19 methyl groups of steroids (or the rate of rotation of methyl groups attached to structurally related, hindered quaternary carbon atoms) at ca. room temperature (either experimental or theoretical). (iii) finally, I am seeking information/references on the RELATIVE rates of rotation of perhydro and isotopically substituted methyl groups. For example, what would one expect to be the rate of rotation of a chiral methyl group (CHDT) RELATIVE to a nonchiral perhydro methyl group (CH3) in the same molecule at the same temperature? I thank all responders for generously sharing their information/calcula- tions with me. Yours respectfully, (Dr.) S. Shapiro Institut fuer orale Mikrobiologie und allgemeine Immunologie Zentrum fuer Zahn-, Mund-, und Kieferheilkunde der Universitaet Zuerich Plattenstrasse 11 Postfach CH-8028 Zuerich, Switzerland Internet: toukie@zui.unizh.ch FAX-nr: ( ... + 1) 261'56'83 From palres.dnet.sandoz.com!bowlus@sandoz.com Thu Nov 3 11:23:31 1994 Received: from tigger.jvnc.net for palres.dnet.sandoz.com!bowlus@sandoz.com by www.ccl.net (8.6.9/930601.1506) id LAA02137; Thu, 3 Nov 1994 11:03:36 -0500 Received: from sndzeh.UUCP by tigger.jvnc.net with UUCP id AA06240 (5.65c/IDA-1.4.4 for chemistry@ccl.net); Thu, 3 Nov 1994 11:03:31 -0500 Message-Id: <199411031603.AA06240@tigger.jvnc.net> Date: Thu, 3 Nov 94 10:56:06 -0500 From: bowlus@palres.dnet.sandoz.com (Steve Bowlus) To: "chemistry@ccl.net"@SNDZEH.dnet.sandoz.com Cc: BOWLUS@sandoz.com Subject: Amsol performance A couple of weeks ago, I wrote: >>>> I am running Amsol 4.5 on an Indigo2 (150Mhz), trying to do solvation energies of compounds with ca. 15 heavy atoms. These systems optimize for the gas phase in about 2 cpu minutes using the keyword "AM1". For the solvation, I am using "AM1 SM2" and 4 cpu _hours_ later, things are still chugging along. I have no experience with the solvation models, and would like know what order of magnitude of cpu times I should be expecting. Also , are there keyword combinations which will reduce this (I haven't tinkered with e.g. PULAY, since the gas phase calculation went so quickly)? >>>> Here are the interesting replies. Note particularly Cramer's remarks. I have also appended a summary of my experience. **** I have used Amsol on an SGI 380 running as single user - my cpds were peptides - 6 residues - and Amsol AM1 SM2 combination run for 1 week without convergence. This was with Amsol 3, to be correct. Using Amsol 4.0 on Ala-Ala took a several hrs on a R4400 Challenge M Generally, it is known to take a long time to converge. Authors of Ampac 5.0 (Semichem - Andy Holder) claim their implementation of Amsol is much faster. Never tried it, though. One suggestion made by Christopher Cramer was to do AM1 SM2 1SCF on the gas optimized cpd - to have an idea of solvating that conformer. Tudor **************************************************************************** * Tudor I. Oprea, MD PhD Tel: (505) 667 2682 * * Postdoctoral Research Associate Fax: (505) 665 3493 * * Theoretical Biology and Biophysics (T-10) Email: * * Los Alamos National Laboratory tudor@t10.lanl.gov * * Mail Stop K710, Los Alamos NM 87545 * **************************************************************************** ***** I observed similarly long run-times in my limited experience with AMSOL. If it's not too much trouble, would you please forward any useful replies you receive to: pearlman@vax.phr.utexas.edu ? Thanks a lot. -- Bob Pearlman ***** I feel I can answer this question fairly authoritatively . . . The SMx solvation models as presently designed do not allow for analytical first derivatives. We are working on this, but for the moment the only way to do an optimization is by brute force finite differences. (Actually, even the gas-phase optimizations are not truly analytical, but they get away with a trick at the NDDO level that fails to be useful for solvation). While this might sound depressing, there is a flip side to the coin. As a rule, reoptimization in solution adds less than 5% to the total solvation free energy relative to that calculated for the gas-phase geometry (the only exception is for very polarizable systems, where small geometrical changes can allow significant distortion of the electronic structure). Many reports in the literature have appeared to this effect by other authors using our models, and we have made these observations too (I'll send you refs if you want, but don't want to waste bandwidth on the net). Since that 5% is typically smaller than the intrinsic error in the model, it is negligible. The frozen geometry calculations only take a few cpu seconds for a system of the size you mentioned, so it is trivial to do the 1SCF calculations, and then decide if you want to invest more time in the full optimization. I add as a final caveat that we are always skeptical about semiempirical geometries after having found time and again some fairly dramatic error in structure (especially intramolecular hydrogen bonds, five-membered rings, amides, and transition states that can exhibit biradicaloid character). Our preferred approach these days is to optimize at a more trustworthy level (depending on your system, that may be anything from a force-field to converged QM calculations) and then add solvation from an SMx calculation at that frozen geometry. In closing, there are electrostatics-only continuum models that permit analytical energy derivatives (e.g., the rather crude Onsager model available in G92 and more refined versions that I believe are slated for release sometime relatively soon, also Tomasi's PCM approach or Rivail's multipole expansion in idealized cavities, coded into GAMESS-UK and the former perhaps in MONSTERGAUSS). If you are dealing with molecules that do not have stationary gas-phase structures (e.g., an amino acid zwitterion) then you might consider such an approach. The virtue of the SMx models, however, is that they have been developed to simultaneously account for non-electrostatic solvation effects, and thus predict solvation free energies that may be compared directly to experiment (Version 4.5 contains only water models, soon-to-be-released version 5.0 also contains hydrocarbon models, other solvents are in various stages of current development). Best regards, Chris P.S. You'll find the above summarized into one sentence in section 8 of the users' manual (which illustrates a nameless universal truth . . . ) -- 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 A later exchange between Cramer and myself: > I'm prepared for > significant time penalties for a 2 minute run (1+ order of magnitude), but > the 2-3 that we seem to be seeing is borderline acceptable. We feel this > is something needed to do, though, since we are (among other things) > comparing the method to COSMO, which is fast if nothing else. > COSMO is a pretty method, although I would say it suffers from (i) unoptimized radii for defining the dielectric boundary and (ii) it is, of course, a pure electrostatic model and unable to handle the non-electrostatics. Andreas Klamt was through here recently, and we had some interesting discussions on some of these issues. We also compared the two programs, and decided that the generalized Born solution to the Poisson equation, and his Green's function approach, give much the same answer for equivalent atomic radii. Incidentally, Don and I wrote a review of continuum methods for Rev. Comp. Chem. and, if the damn volume ever comes out (it's only been 17 months now) we made a fairly large comparison between COSMO and various other methods, including our own. Bottom line was that COSMO seemed to slightly overpolarize things, in our opinion, but otherwise correlated nicely with SM2 solvation free energies. If you'd like, I'll send you a preprint of that chapter. > Thanks for the information. My first job ran about 5.5 cpu hours, but the > second (an amide. . .) is 15 and counting. > In the superstitious tricks that you might find useful category, it often turns out that a small perturbation from the gas-phase geometry (say 0.1 angstroms in one bond length) helps speed convergence. That is because the default optimizer in AMPAC is sometimes a bit confused when it is started out very near a minimum-energy geometry. It thrashes around a lot before deciding it was in a pretty good spot to begin with. On the other hand, if it has at least one decent gradient to minimize, it seems to consider itself to have converged more effectively. If you can spare the time, you might want to try such an approach on your recalcitrant amide and see if it helps. Best regards, Chris -- 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 ***** Now, my experience: I have made 20 runs with molecules ranging from 16 to 24 heavy atoms. I have a range of cpu times from 1.3 to 20 hrs on an 150 MHz Indigo2, with a mean of 7-8. Of the runs, 4 were longer than 15 hours, 8 were 5 hours or less. I don't know how "fair" this test is or how "typical" my molecules are -- although they are quite typical for ag chem ;-) -- as Cramer comments, there did appear to be some thrashing about but I did not see any correlation in run-time with atom count, specific functional groups, etc. I haven't checked the values for 1SCF solvations of the gas phase structures for most of the compounds, but if the values are acceptable, this will be a blessing: the run time is only on the order of a minute. sb =========================================================================== Stephen B. Bowlus, Ph.D. Computer-Aided Molecular Design Research Division e-mail: bowlus@sandoz.com Sandoz Agro, Inc. Phone: + 1 415 354 3904 975 California Ave. Fax: + 1 415 857 1125 Palo Alto, CA 94304 =========================================================================== From oesterei@hrz.ba-freiberg.de Thu Nov 3 12:23:27 1994 Received: from orion.hrz.ba-freiberg.de for oesterei@hrz.ba-freiberg.de by www.ccl.net (8.6.9/930601.1506) id LAA03723; Thu, 3 Nov 1994 11:46:23 -0500 Message-Id: <199411031646.LAA03723@www.ccl.net> Received: by orion.hrz.ba-freiberg.de (16.6/15.6) id AA09101; Thu, 3 Nov 94 17:43:00 +0100 From: Ralf Oestereich Subject: Still: SPARTAN and COLLAGE for printing? To: chemistry@ccl.net (Computer Chemistry List) Date: Thu, 3 Nov 94 17:42:59 MEZ Mailer: Elm [revision: 66.25] Dear Netters. As I read before, it is possible to use "collage" to make some printing with SPARTAN. Well, I got the collage files from an FTP server, we installed it in the AVS-programm, but---- what now? Can explain us, how we can use collage for SPARTAN? This would help us very much!!! Thank you in advance, R. Oestereich member of Inorganic Divison of the Bergakademie Freiberg, Germany From cletner@remcure.bmb.wright.edu Thu Nov 3 13:23:29 1994 Received: from remcure.bmb.wright.edu for cletner@remcure.bmb.wright.edu by www.ccl.net (8.6.9/930601.1506) id NAA04997; Thu, 3 Nov 1994 13:04:46 -0500 Received: by remcure.bmb.wright.edu (931110.SGI/921111.SGI.AUTO) for CHEMISTRY@ccl.net id AA01750; Thu, 3 Nov 94 12:55:25 -0800 Date: Thu, 3 Nov 1994 12:44:10 -0800 (PST) From: Charles Letner Subject: More AMBER atom types To: Computational Chemistry List Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, I just finished reading the summary of kd7@tower.york.ac.uk about atom types in AMBER. It seems that this approach of taking a atom type >from the AMBER force field and using this as an atom type in a non-protein molecule is OK. However, I'm wondering how general this is. I'm planning on including substrates in some of my upcoming MDs. As these only contain C, H, N, and O, I can probably find similar atoms among the standard atoms of AMBER. So, is this reasonable or should I still think about creating new parameters (ala tha Hopfinger & Pearlstein, 1984 article)? I'd be very interested in opinions as well as aspects that should be considered when making this decision. Thanks for your time, Chuck Charles Letner Wright State University Department of Biochemistry Dayton, OH 45435 e-mail: cletner@remcure.bmb.wright.edu From garciae@ucsub.Colorado.EDU Thu Nov 3 14:26:00 1994 Received: from ucsub.Colorado.EDU for garciae@ucsub.Colorado.EDU by www.ccl.net (8.6.9/930601.1506) id OAA06076; Thu, 3 Nov 1994 14:08:07 -0500 Received: (from garciae@localhost) by ucsub.Colorado.EDU (8.6.9/8.6.9/CNS-3.5) id LAA36154; Thu, 3 Nov 1994 11:50:58 -0700 Date: Thu, 3 Nov 1994 11:50:29 -0700 (MST) From: Garcia Edgardo To: CHEMISTRY@ccl.net Subject: CCL: Torsional potentials Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi netters, I'm doing some calculations in torsional barriers using semiempirical(AM1/PM3) and ABinitio (HF level) methods. I noticed that AM1 and PM3 results are very diferent, not only in the relative values but also in the shape of the profiles, different minima and maxima. (I am using Spartan 3.1 implementation with full geometry optimization for each dihedral) o AM1 seems to be in better agreement with experimental and ABinitio results (qualitative). o PM3 seems to give too little importance to conjugation, or to over estimate VDW steric interactions, giving wrong locations for the minima and maxima. o PM3 gives some sudden changes in energy of some points in the torsional profiles. The question is, PM3 is a latter parametrization, why it's not giving better results than AM1 (at least for this type of calculations) ? If you can point some references on ABinitio calculations of torsional potentials for: Benzo Phenolates, Esters, Ethers, and Halide and Ciano Alkils, I would appreciate a lot. Thanks, Edgardo Garcia Cristol Chem. & Biochem. Univ. of Colorado Boulder CO USA From KEWISE@aardvark.ucs.uoknor.edu Thu Nov 3 14:31:23 1994 Received: from aardvark.ucs.uoknor.edu for KEWISE@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.9/930601.1506) id OAA06105; Thu, 3 Nov 1994 14:11:03 -0500 From: Message-Id: <199411031911.OAA06105@www.ccl.net> Date: Thu, 3 Nov 94 13:11 CST Subject: Summary of MOPAC 6.0 C.I.Convergence Question To: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" Hello again, I recently posted a request for suggestions on achieving convergence in MOPAC 6 configuration calculations, to which I recieved to following replies. I am in the process of trying some of the ideas out and if anyone is interested I can let them know what worked the best. One additional question: who distributes MOPAC 93 and what does it cost? I've seen MOPAC 7 on www.ccl.net but have not been able to locate MOPAC 93. At any rate, here are the responses. Thanks again to all who replied. Kristopher Wise Univeristy of Oklahoma Department of Chemistry and Biochemistry KEWISE@aardvark.ucs.uoknor.edu ******************************************************************************** From: IN%"grzesb@asp.biogeo.uw.edu.pl" 2-NOV-1994 05:02:33.94 To: KEWISE@aardvark.ucs.uoknor.edu CC: Subj: I am NOT sure if MOPAC 6.0 does correctly C.I> As I know in MOPAC 93 ( or MOPAC 7) people changed much in the code calculating C.I. So try to use newer version or at least conntac Dr Stewart ( the author of MOPAC ) Best wishes G.Bakalarski (Poland) ******************************************************************************** From: IN%"frj@dou.dk" "Frank Jensen" 1-NOV-1994 06:09:47.65 To: kewise@aardvark.ucs.uoknor.edu CC: Subj: mopac ci optimizations A couple of points: 1) Do you really need geometries converged to less than 1.0 kcal/mol? The energy should be stable to ~ 0.01 kcal/mol with a grad.norm of this size. Relative energies of "accuracies" of 0.01 kcal/mol has no meaning in semiempirical calculations, the inherent error is much larger. 2) If you really need this tight convergence, ypu need to take care that the gradients actually are calculated to an accuracy which allows small steps, i.e. convergence to less than 1.0 may involve geometry steps of maybe 0.0001 Ang or less. Make sure that gradients are actually calculated sufficiently accurate, i.e. tighten up the SCF convergence and use the analytical CI gradient option. 3) EF will work if you provide it with a good Hessian, specifying HESS=1 will calculate the Hessian at the first step. This is expensive at the CI level, you may try to use a Hessian from the RHF wave function, and just read it in for use at the CI level. 4) if these options do not work, I'll be happy to take a look at your problem. Frank ******************************************************************************** From: IN%"o-cha@cnj.digex.net" "Matthew E. Harbowy" 31-OCT-1994 23:12:58.09 To: KEWISE@aardvark.ucs.uoknor.edu, chemistry@ccl.net CC: Subj: CCL:Convergence in MOPAC C.I. calculations >I am using MOPAC 6.0 to do calculations on fairly large polycyclic >molecules related to porphyrins. Part of this work involves optimizing >geometries and calculating energies for the cations and anions of these >molecules. To make these calculations more accurate (hopefully) we are >using the configuration interaction options in MOPAC 6, but have encountered >some problems with convergence. After reducing the gradient to below 1.0, It's a great idea, one that i've tried to rationalize myself. It's also a double correction, since parameterization adjusts the energies to include the 'correlation' piece once already, and what that means for transition states is anyone's guess. >the optimization begins to oscillate, and shows no sign of convergence >after running for several hours. A typical command line is as follows: > >AM1 PRECISE CHARGE=-1 C.I.=(4,2) VECTORS NODIIS Indeed, I saw the same thing, and EF only makes it worse. NLLSQ was the one that did the trick, and occasionally I would use SIGMA as well. Also, you have to be very careful about picking your ci levels. sometimes (5,2) is a much better choice due to near degeneracies which don't cause it to abort with errors, but oscillate instead. Also, try dummy atoms, and define your geometries in different ways. A well chosen zmatrix cured some, not all, of my ills. Part of my problem turned out to be I was attributing more symmetry to the molecule than was true by a bad zmatrix definition. XYZ was right out because I was studying a cyclization, and the orchestrated nature of the reaction required good control of the zmatrix. I assume for porphyrin analogs you're using symmetry to cut down on the number of dependent variables. what I found was the forced symmetry led me to a multiple saddle point, not a minimum or transition state. >Kristopher Wise >University of Oklahoma >Department of Chemistry and Biochemistry >KEWISE@aardvark.ucs.uoknor.edu matt harbowy tea chemist, thomas j lipton. -- matt harbowy | o-cha@cnj.digex.net | "I'm the bear that went greentea@eden.rutgers.edu | over the mountain." harbowy@aol.com | ******************************************************************************** From: IN%"davem@hydra.convex.com" 31-OCT-1994 14:06:18.73 To: KEWISE@aardvark.ucs.uoknor.edu CC: Subj: Re: CCL:Convergence in MOPAC C.I. calculations Hello Kristopher, I don't think that the analytical CI gradients really work in MOPAC 6.0. Please try the NOANCI keyword. This should give you better gradients. Dave Mullally Convex Computer Corp. ******************************************************************************** From: IN%"rgab@trpntech.com" "Richard Bone" 31-OCT-1994 12:41:09.49 To: KEWISE@aardvark.ucs.uoknor.edu CC: Subj: Re: CCL-Convergence in MOPAC If I understand from your message correctly that you are experiencing problems in converging geometry optimizations (irrespective of level of theory) I refer you to my ERROR-correction notice, published in QCPE bulletin, February 1994 (Vol. 14, No. 1, p.10). I think that this should fix you up. Richard Bone Richard G. A. Bone, PhD. Computational Chemist Terrapin Technologies, Inc. South San Francisco USA E-mail rgab@trpntech.com From longshot@chem.duke.edu Thu Nov 3 16:23:29 1994 Received: from duke.cs.duke.edu for longshot@chem.duke.edu by www.ccl.net (8.6.9/930601.1506) id PAA09000; Thu, 3 Nov 1994 15:35:36 -0500 Received: from london.chem.duke.edu by duke.cs.duke.edu (5.65/3.10G/4.1.3) id AA20458; Thu, 3 Nov 94 15:35:30 -0500 Received: from canada.chem.duke.edu by london.chem.duke.edu (5.64/1.19LP/4.1.1) id AA10216; Thu, 3 Nov 94 15:35:29 -0500 Received: by canada.chem.duke.edu (5.64/2.12L/4.1) id AA11566; Thu, 3 Nov 94 15:35:28 -0500 Date: Thu, 3 Nov 94 15:35:28 -0500 From: longshot@chem.duke.edu (Brad Isbister) Message-Id: <9411032035.AA11566@canada.chem.duke.edu> To: chemistry@ccl.net Subject: Re: CCL:More AMBER atom types Charles Letner writes about the selection of atom types in AMBER. The selection of atom types should always use a data set which resembles the compounds to be investigated. The original AMBER parameters which were derived for proteins and nucleic acids are pretty good for the functional groups found in such systems (peptide backbone, AA sidechains, C, T, G, A, etc). If your system includes other functional groups, a literature search for AMBER parameters which better reflect the 'real' system is a good idea. These new atom types can be included in an frcmod file for addition to the standard parameter set. Several papers have been written on 'non-standard' functional groups. In my work, I use the parameters for carbohydrates from S.W Homans, Biochemistry, 1990, 29, 9110-9118. If you want to know just what compounds were used to derive the standard AMBER parameter set, get the original AMBER papers: Kollman, Case, et al, JACS, 1984, 106, 765-784 and Kollman, Case, et al, J. Comp. Chem., 1986, 7, 230-252. You should also look in the AMBER manual p23-24 for more info on the parameter databases. I've seen rumblings of "Does anyone(else) want to set up a database of published AMBER parameters (or references to such)?" But I don't think anyone has taken the plunge and volunteered. There is always the possibility that your compound is very different from anything you can find. In that case, refer to some papers on deriving atom, bond, angle, and torsion parameters from spectroscopic data and/or Quantum Mechanical simulation. I haven't had to go that route yet. Perhaps some others on the CCL can help out with the references? In the end, Molecular Mechanics is a game of assumptions. Too many guesses and your results are worthless or misleading; too few and you'll be running very long and inefficient simulations. You'll have to determine how similar the database compounds are to the compound of interest. Good Luck! -Brad ---------------------------------Clip N Save------------------------------------ Brad Isbister Duke University longshot@chem.duke.edu Department of Chemistry Computational/Biophysical chemistry E.J. Toone group From helden@gaucho.ucsb.edu Thu Nov 3 21:23:32 1994 Received: from hub.ucsb.edu for helden@gaucho.ucsb.edu by www.ccl.net (8.6.9/930601.1506) id UAA13169; Thu, 3 Nov 1994 20:52:58 -0500 Received: from gaucho.ucsb.edu by hub.ucsb.edu; id AA24448 sendmail 4.1/UCSB-2.1-sun Thu, 3 Nov 94 17:52:41 PST for chemistry@ccl.net Received: by gaucho.ucsb.edu (AIX 3.2/UCB 5.64/4.03) id AA23033; Thu, 3 Nov 1994 17:51:23 -0800 From: helden@gaucho.ucsb.edu (Gert von Helden) Message-Id: <9411040151.AA23033@gaucho.ucsb.edu> Subject: ff parameters for alkali ions To: chemistry@ccl.net Date: Thu, 3 Nov 1994 17:51:22 +22305458 (PST) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 774 Hi, I am looking for force field parameters for alkali ions. I am using Sybyl and a couple (Li+, Na+..) are build in. However I would be interested in Cs+, which is not in there. What I need to put it in is: a)vdw radius b)electronegativity and c) "temperature factor" (have no idea what that is). Does anybody have either references or parameters for alkali ions? How do they get determined anyway? thanks, Gert ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Gert von Helden, Dept. of Chemistry, UCSB, Santa Barbara, CA 93106 + + Tel : 805-893-2673, Fax : 805-893-8703 + + E-mail: helden@gaucho.ucsb.edu + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From YQIN@aardvark.ucs.uoknor.edu Thu Nov 3 23:23:34 1994 Received: from aardvark.ucs.uoknor.edu for YQIN@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.9/930601.1506) id WAA14223; Thu, 3 Nov 1994 22:52:22 -0500 From: Message-Id: <199411040352.WAA14223@www.ccl.net> Date: Thu, 3 Nov 94 21:53 CST Subject: Protein data bank To: chemistry@ccl.net X-VMS-To: IN%"chemistry@ccl.net" Dear Netters: I am interested in to get some structures of protein from protein data bank. But I have some probelm to get in touch with the data bank. Can somebody give me direction how and where I can get in touch with protein data banki( I mean email address or whatever). Thank you all for your help. With my best regards yue qin yqin@aardvark.ucs.uoknor.edu