From chemistry-request@ccl.net Fri Jun 26 04:53:50 1992 Date: Fri, 26 Jun 92 08:28:04 +0200 From: martin@biokth.sunet.SE Subject: Cut offs. To: "chemistry@ccl.net"@kth.sunet.SE Status: RO Hi, To my knowledge there are not many studies of how to treat cutoffs in the literature. However in Proteins: Struct. Funct. Genet. 6:32-45 (1989) there is a quite extensive study. They have used the CHARMM force field, however I think this may account for any similar force field. My opinion is that the cutoffs that one has to use is very dependent on how the electrostatics of the calculation is treated. I'm a Sybyl User that use the AMBER FF in Sybyl for dynamics and mechanics calculation of biomolecules. For vacuum calculations I use a cutoff of 10-12 A (distance dependent dielectric constant) and 8-10 A for solvent calculations. The effect of the cutoffs to the vdW forces is less important I think. These long range vdW forces does not have any large impact on the structure, but may of course change the total energy level of a calculation. Finally, I think that what may become even more important is to include polarizability to the electrostatics, especially for biomolecules. Not before that becomes real we will treat simulations of biomolecules in the best possible way. I have heard from a colleague about a new structure of an ion transporting protein which had a narrow channel where in one the sides of this channel it was up to 5-7 lysines or arginines and the other side contained about 4 aspartates or glutamates. These residues were clustered very near eachother. Would anybody think that a molecular dynamics simulation of this protein would be succesful using todays standard force fields ? I hesitate...... Any comments to the net regarding these questions would be very much welcomed by me, because I think it is very important for the improvement of the MD techniques in biological chemistry (which I think and hope is and will be a very useful tool). Greetings Martin Norin KTH Stockholm e-mail:martin@physchem.kth.se From chemistry-request@ccl.net Fri Jun 26 10:17:06 1992 Date: Fri, 26 Jun 92 13:29:53 ITA From: Davide Proserpio To: CHEMISTRY@ccl.net Status: RO Hi, I am looking for the program describe on Science vol 253, 1991 p 164 - A Method to Identify Protein Sequences That Fold into a Known 3D Structure - by J.U. Bowie, R.Luthy and D. Eisenberg Anyone knows if it is available somwhere? Thanks **************************************************************** Davide M. Proserpio UNIVERSITA' DI MILANO ISTITUTO DI CHIMICA STRUTTURISTICA INORGANICA VIA VENEZIAN 21, 20133 MILANO - ITALY PHONE : 39-2-70635120 FAX : 39-2-70635288 E-MAIL: STINCH AT IMISIAM.MI.CNR.IT **************************************************************** From chemistry-request@ccl.net Fri Jun 26 10:44:46 1992 Date: Fri, 26 Jun 92 08:33:55 -0400 From: markm@charles.polymer.uakron.EDU (Mark Alan Matties) Subject: g90 manual? To: chemistry@ccl.net Status: RO to all, would someone be kind enough to send me the address from where i can order a gaussian90 manual? thanks, mark ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ mark alan matties u of akron markm@iris.polymer.uakron.edu dept of polymer science "aoibheann beatha an scola/ire" akron, ohio, usa From chemistry-request@ccl.net Fri Jun 26 11:19:23 1992 Date: 26-JUN-1992 10:17:15.95 From: WSONNEN@EAGLE.WESLEYAN.EDU Subject: NEW HELIX PROGRAM To: chemistry@ccl.net Status: RO Dear Netters, I would like to obtain a copy of the program by R. E. Dickerson's lab: NEW HELIX 90 (or whatever the latest version is). I would very much appreciate getting the e-mail address of (??) where i can obtain this program. Thank you, Wayne Sonnen wsonnen@eagle.wesleyan.edu From chemistry-request@ccl.net Fri Jun 26 14:26:59 1992 Date: Fri, 26 Jun 92 09:55:16 PDT From: yuan@picasso.mmwb.ucsf.EDU To: chemistry@ccl.net, wsonnen@eagle.wesleyan.EDU Status: RO Dear Netters, Here is the e-mail address for 1992 NEWHEL helix analysis program. D. Dickerson's e-mail: red@uclaue.mbi.ucla.edu Yate-Ching Yuan Thomas James's Lab. ---------------------------------------------------------------------------- Dr. Yate-Ching Yuan Department of Pharmaceutical Chemistry Tel. 415-476-1569 Mail Stop 0446 Fax 415-476-0688 University of California internet: yuan@picasso.mmwb.ucsf.edu San Francisco, CA 94143-0446 ---------------------------------------------------------------------------- From chemistry-request@ccl.net Fri Jun 26 18:03:15 1992 Date: Fri, 26 Jun 92 15:39:11 EDT From: rs0thp@rohmhaas.COM Subject: ACS COMP News available (PostScript) from Chemistry To: chemistry@ccl.net Status: RO Dear Folks, The Newsletter of COMP Division of Americal Chemical Society is now available in electronic form from the Computational Chemistry List archives. Current contents are: Volume 17 # 1 COMP News Editorial .. . . . . . . . . . . . . . . . . . . . . . . . . 2 Chairman's Corner . . . . . . . .. . . . . . . . . . . . . . . . . 2 COMP Officers . . . . . . . . .. . . . . . . . . . . . . . . . . 3 Future Symposia . . . . . . . . ... . . . . . . . . . . . . . . . .4 COMP Program for Graduate Students.......... . . . . . . . . . . . 5 Upcoming Meetings . . . . . . . . . .. . . . . . . . . . . .5 Notes from InterNet . . . . . . . . . . . . . . . . . . . . . .9 Access to Information on InterNet. . . . . . . . . . . . . 9 Selection of Non-bonded Cutoffs .. . . . . . . . . . . . . 9 New Journal for Computational Chemistry? . . . . 11 Numerical Data Request . . . . . . . . . . . . . . . . . 14 Successes in Computational Chemistry . . . . . . . . 15 Change in Chemistry Archives . . . . . . . . . . . . . 16 C vs Fortran Summary . . . . . . . . . . . . . . . . . 16 Full Abstracts for Washington Meeting .. . . .. . . . . . . . . . 17 COMP Division Email Request . . . . . . . . . . . . . . . . . 33 It is available in two formats: a) the plain text format (vol17.txt) and in PostScript(vol17.ps){PostScript file is better since it is supposed to be two column format...}. Please note that the file with text version is much smaller than the PostScript one, so you should retrieve this file if you are using e-mail interface to Comp.Chem.List archives. How to get it? For those who are blessed with ftp: %ftp www.ccl.net (or ftp 128.146.36.48) Login: anonymous Password: Your_e-mail_address ftp> cd pub/chemistry/comp_news ftp> get vol17.ps (if you have a PostScript Printer) or ftp> get vol17.txt (if you do not have PostScript Printer) ftp> quit For those who have only an e-mail access, send one line message: send ./comp_news/vol17.txt from chemistry to OSCPOST@ccl.net or OSCPOST@OHSTPY.BITNET and the newsletter in a text format will be automatically forwarded to your mailbox. Many Thanks to Jan Labanowski for setting this up, and I hope this helpful to you. -- Sincerely, Thomas Pierce, thpierce@rohmhaas.com or rs0thp@rohvm1 Official Disclaimer:"The opinions expressed are those of the writer and not the Rohm and Haas Company." From chemistry-request@ccl.net Fri Jun 26 18:11:00 1992 Date: Fri, 26 Jun 92 16:24 EDT From: SML108@PSUVM.PSU.EDU Subject: profiles To: STINCH%IMISIAM.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU Status: RO Contact David Eisenberg: david@uclaue.mbi.ucla.edu Scott From chemistry-request@ccl.net Fri Jun 26 20:11:45 1992 Date: Fri, 26 Jun 1992 20:11 EDT From: tripos!metis!matt@uunet.UU.NET (Matt Clark) Subject: Re: Sybyl FF followon To: uunet!ccl.net!chemistry@uunet.UU.NET Status: RO Date: Fri, 26 Jun 92 16:47:38 EDT Sender: chemistry-request@ccl.net Errors-To: owner-chemistry@ccl.net Precedence: bulk In response to Joe Leonard's questions... 1) The cutoff is not required for single-molecule or non- bounded calculations; the energy is the most accurate if the cutoff is set to something larger than the molecule. Of course you pay the penalty in time required since the number of non-bonded pairs increases. For simulations with periodic boundary conditions some kind of cutoff is necessary, or Ewald summation is used in some programs. 2) I agree with Damodaran in that 8 Angstroms might not be suitable for all cases, but it seems to work for most situations. The vdw energy drops off very rapidly and the energy difference with and without cutoffs is small. I'm an empiricist, so I did some calculations to see how big a difference cutoffs make. Here are some energies computed for crambin (1crn) with all hydrogens added, without any minimization. (TRIPOS 5.2 force field, but Hydrogen vdw radius is 1.2 Angstroms; Kollmann all-atom charges, constant dielectric) SYBYL, like AMBER uses a residue-based cutoff; if any atom in a residue is within the cutoff distance from another, all atoms in both residues are used in the non-bonded calculations. Cutoff vdW E Electrostatic E # pairs 100 691.245 -2684.925 197,287 8 692.740 -2683.961 91,773 The 100 Angstrom cutoff takes about twice as long and increases the accuracy by about 0.2%. Bernard Brooks did a lot of work to see how different cutoffs affected dynamics trajectories. I believe this is what Martin Norin is referring to. 3) There has been one change since the TRIPOS force field paper, involving the handling of hydrogen bond pairs. In the paper the vdw term for the two atoms forming the hydrogen bond was set to zero so that the two atoms can move closer together and lower the electrostatic energy. We found that in dynamics the two atoms involved in the hydrogen bond had a tendency to "fuse" so that the coulombic energy was infinite; now we scale down the sum of the vdw radii used in the vdw term by 70%. From chemistry-request@ccl.net Fri Jun 26 23:45:30 1992 Date: 26 Jun 92 21:40:00 EDT From: "STEPHEN R. HELLER" Subject: NEw ACS Book Series To: chemistry Status: R 26 June, 1992 ANNOUNCEMENT The ACS has just initiated a new Computers in Chemistry - Reference Book Series. I have been appointed over-all editor of the series. The goal of the ACS is to produce a series of books which will be useful reference books in various areas of computer chemistry. This is NOT a book series for symposia or other highly timely, but narrow areas. The ACS will continue to publish the ACS Symposium Series of books. Each book in the series will be written and/or edited by various individuals who are experts in their respective areas of computer chemistry. This note is a "call for authors". I would like to hear >from anyone who is interested in writing or editing a book for this series. A number of areas come to mind, such as: 1. Applications of Super Computers 2. Telecommunications/Computer Networks 3. Molecular Modeling/Drug Design 4. LIMS 5. Polymer Modeling 6. Neural Networks 7. Data Analysis/Curve Fitting Software 8. 2D/3D Structure Searching 9. Data Standards/Data Exchange/Interchange If anyone is interested in this project, please contact me by INTERNET, mail, FAX, or phone: Stephen R. Heller Informatics Project Leader Plant Genome Research Program USDA, ARS, BARC-West Building 005, Room 337 Beltsville, MD 20705-2350 USA Phone: 301-504-6055 FAX: 301-946-2704 INTERNET: SRHELLER@ASRR.ARSUSDA.GOV To initiate a book for this series I will need, at least, a tentative title, outline, list of chapters, and authors.