From mcblimts@leonis.nus.sg Mon Oct 30 01:15:43 1995 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id BAA04521; Mon, 30 Oct 1995 01:10:47 -0500 Received: from leonis.nus.sg (root@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id OAA10375; Mon, 30 Oct 1995 14:10:35 +0800 Received: from ([137.132.42.122]) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with SMTP id OAA22623; Mon, 30 Oct 1995 14:10:34 +0800 Date: Mon, 30 Oct 1995 14:10:34 +0800 Message-Id: <199510300610.OAA22623@leonis.nus.sg> X-Sender: mcblimts@leonis.nus.sg Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: mcblimts@leonis.nus.sg (Lim Teck Sin) Subject: phi,psi computation Cc: mcbgane@leonis.nus.sg, wlawton@iss.nus.sg X-Mailer: Status: R Hi everyone, Does anyone know if there exists programs which compute phi, psi angles of peptide backbones, given the xyz coordinates of atoms in pdb format? Thanks. Will summarise reply if necessary. best regards - teck sin From owner-chemistry@ccl.net Mon Oct 30 09:00:52 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id IAA10488; Mon, 30 Oct 1995 08:57:47 -0500 Received: from comm1.ab.umd.edu for alex@mmiris.ab.umd.edu by bedrock.ccl.net (8.6.10/950822.1) id IAA04323; Mon, 30 Oct 1995 08:57:45 -0500 From: Received: from mmiris.ab.umd.edu (mmiris.ab.umd.edu [134.192.31.160]) by comm1.ab.umd.edu (8.6.12/8.6.12) with SMTP id JAA21393; Mon, 30 Oct 1995 09:01:08 -0500 Received: by mmiris.ab.umd.edu (931110.SGI/911001.SGI) for @comm1.ab.umd.edu:chemistry@ccl.net id AA23708; Mon, 30 Oct 95 08:57:45 -0500 Date: Mon, 30 Oct 95 08:57:45 -0500 Message-Id: <9510301357.AA23708@mmiris.ab.umd.edu> To: Andrey.Bliznyuk@anu.edu.au Cc: chemistry@ccl.net, Andrey.Bliznyuk@anu.edu.au In-Reply-To: "Andrey Bliznyuk"'s message of Mon, 30 Oct 1995 10:27:03 <199510300042.LAA00381@anugpo.anu.edu.au> Subject: CCL:Charmm atomic charges, where to find them? Status: R Andrey, There are new charmm parameters for nucleic acids, proteins and lipids. your best bet would be to use those. do you have access to a recent version of charmm. they are included with the program. otherwise, I can send them to you. Alex Alex MacKerell, alex@mmiris.ab.umd.edu School of Pharmacy University of Maryland at Baltimore 20 North Pine Street Baltimore, MD 21201 410-706-7442 From owner-chemistry@ccl.net Mon Oct 30 13:15:54 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id NAA16688; Mon, 30 Oct 1995 13:01:42 -0500 Received: from phyas1.mps.ohio-state.edu for L330%SUEARN2.BITNET@mps.ohio-state.edu by bedrock.ccl.net (8.6.10/950822.1) id NAA06467; Mon, 30 Oct 1995 13:01:40 -0500 From: Received: from SUEARN2.BITNET (MAILER@SUEARN2) by MPS.OHIO-STATE.EDU (PMDF V5.0-4 #9122) id <01HX1W2TXMPC8WVZ27@MPS.OHIO-STATE.EDU> for CHEMISTRY@ccl.net; Mon, 30 Oct 1995 13:01:40 -0500 (EST) Date: Mon, 30 Oct 1995 20:56 +0000 (MSK) Subject: CCL:G94: Parallel Cray and DEC AXP OpenVMS versions To: CHEMISTRY@ccl.net Message-id: <01HX1W2U046A8WVZ27@MPS.OHIO-STATE.EDU> Content-transfer-encoding: 7BIT Status: R Dr. D.J. Moses wrote in his letter: > Gaussian, Inc is pleased to announce the availability of Gaussian 94 > for parallel Cray C90, YMP and J90 systems and DEC Alpha OpenVMS systems. Does somebody know the results (execution times) of test 178 parallelization for DEC systems, for example, for DEC AlphaServer 8200/8400 ? BTW, what is known about OSF/1 parallel version ? Best regards, N. Anikin, N.D. Zelinsky Institute of Organic Chemistry, Moscow From mcblimts@leonis.nus.sg Mon Oct 30 23:46:02 1995 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id XAA00659; Mon, 30 Oct 1995 23:29:59 -0500 Received: from leonis.nus.sg (root@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id MAA31606 for ; Tue, 31 Oct 1995 12:29:16 +0800 Received: from ([137.132.42.122]) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with SMTP id MAA22875 for ; Tue, 31 Oct 1995 12:29:14 +0800 Date: Tue, 31 Oct 1995 12:29:14 +0800 Message-Id: <199510310429.MAA22875@leonis.nus.sg> X-Sender: mcblimts@leonis.nus.sg Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: mcblimts@leonis.nus.sg (Lim Teck Sin) Subject: parameters of proteins X-Mailer: Status: R Hi Everyone, Does anyone know of programs or Internet sites which have listing of the mol.wt, no.of residues, and/or other parameters of proteins?? Thanks. best regards - tecksin From owner-chemistry@ccl.net Tue Oct 31 10:31:12 1995 Received: from bedrock.ccl.net for owner-chemistry@ccl.net by www.ccl.net (8.6.10/950822.1) id KAA10429; Tue, 31 Oct 1995 10:29:37 -0500 Received: from genie.terra.co.il for rvn@genie.terra.co.il by bedrock.ccl.net (8.6.10/950822.1) id KAA15515; Tue, 31 Oct 1995 10:29:23 -0500 Received: from genie.terra.co.il (localhost [127.0.0.1]) by genie.terra.co.il (8.6.12/8.6.12) with SMTP id PAA01488 for ; Tue, 31 Oct 1995 15:27:14 GMT Message-Id: <199510311527.PAA01488@genie.terra.co.il> Date: Tue, 31 Oct 95 17:27:15 0200 Sender: rvn@genie.terra.co.il From: Reuven Bakalash To: chemistry@ccl.net Subject: New parallel platform for Computational Chemistry TR2000 - A new powerful computing resource for CC ------------------------------------------------- ___________________________________________________________ | * Significant time reduction in long computational tasks| | * A fraction of cost of comparable systems | | * Full range of Software tools | | * A personal computing resource | ----------------------------------------------------------- TR2000 is a desk side parallel computing resource with UNIX front end. 4 to 32 Alpha processors with distributed memory (up to 64MB each). The TR2000 architecture offers a peak performance of 2.5 GFLOPS for Alpha 24064-150 MHz, and 5 GFLOPS for Alpha 24064-275 MHz. The performance scales linearly with each additional processor. TR2000 provides parallel applications in computational chemistry, such as Molecular Dynamics, Lattice Field Theory, Monte Carlo etc. It also provides libraries for porting serial packages. For Molecular Modeling it runs MOIL and CHARMMm23 with exceptional results. Here are comparative figures of leading computers running MbCO + 3830 water molecules (total 14026 atoms), 12-14A shift using FAST option in CHARMm23. All indicated times are in hours (run times are provided by M. Hadocek, NIH): COMP. SYS. # PROC. RUN TIME ---------- ------- -------- SGI/Indy 1 8.93 SGI/Pwr.Indigo2 1 2.93 IBM/SP2 16 0.28 Cray T3D 16 0.77 SGI/PChallenge 16 0.21 TR2000 16 0.65 Status: Two beta-sites are installed at : * Hebrew University, Jerusalem, Ron Alber - since 9/95 * Mount Sinai Medical Center, NY, Harel Weinstein - since 10/95 Prof. Ron Elber recommends(29/10/195): " The Terra-2000 super-workstation gave a significant boost to our abillities to pursue lengthy, numerically intensive calculations. The Terra-2000 - a parallel computer with 16 alpha 150 MHz processors, is employed in our laboratory as a "real" parallel computer running a single task. It is also employed as a cluster of workstations running the same program with different inputs.In both modes, the new computer provides unprecent performance in the workstation area. It makes it possible for us to pursue new calculations with significantly more statistics or simulations of larger systems." Contact: rvn@mail.terra.co.il From rcfort@maine.maine.edu Tue Oct 31 16:01:15 1995 Received: from MAINE.maine.edu for rcfort@maine.maine.edu by www.ccl.net (8.6.10/950822.1) id PAA19508; Tue, 31 Oct 1995 15:50:22 -0500 Date: Tue, 31 Oct 1995 15:50:22 -0500 Message-Id: <199510312050.PAA19508@www.ccl.net> Received: from rfort3.umeche.maine.edu by MAINE.maine.edu (IBM VM SMTP V2R3) with TCP; Tue, 31 Oct 95 15:48:30 EST X-Sender: rcfort@maine.maine.edu (Unverified) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" To: chemistry@www.ccl.net From: rcfort@maine.maine.edu (Raymond C. Fort, Jr.) Subject: Summary of X-clients X-Mailer: Status: R Here is the promised summary of responses on the topic of X-windows clients. Last week I asked the question: >I have recently received an NSF-ILI grant for the purchase of SGI >workstations that will be used to introduce molecular modeling into >the undergraduate and graduate curricula. Our plan is to run SPARTAN, >PCModel, and MacroModel on the workstations; all are available as >X-applications. Then we will provide student access from a Department >PC cluster by running X-terminal emulators on the PCs. >I would be interested to hear from persons who have successfully >applied this kind of connectivity to modeling software, even if >it did not involve the specific programs cited. What X-term >software is best? (We currently are looking at PC-Xware from NCD >and XoftWare from Age). What problems did you encounter? The most common response was to put LINUX on the PCs and use Xfree86. Fred Arnold (fparnold@structures.uchicago.edu), Kris Boulez (kris@bionmrl.rug.ac.be), Carlo Nervi (nervi@chpc06.ch.unito.it), Susan Jackels (sjackels@ac.wfu.edu), Carl David (DAVID@UConnVM.UConn.edu), and Konrad Hinsen (hinsenk@ere.umontreal.ca) suggested this option, and Konrad was good enough to summarize the best points of LINUX: - Cost. Linux is free and doesn't demand huge resources. - Flexibility. A Linux system is an independent (if not very powerful) workstation, which is sufficient for the needs of many students. So we could reduce the number of users on the "big" stations, and offer accounts to more students. - Administration. There is no shortage of graduate students who Linux very well (from running it on their own machines athome). So system administration was not a problem, after the initial installation. - Independence. A Linux system contains its own complete set of X software with fonts etc., whereas an X terminal may need an external font server, thereby increasing network load and creating a dependence on a specific machine (we often had network problem that could cut off some machine from the local Ethernet). This is the solution I will employ for access from my own PC, where I have a half gig LINUX partition installed. However, the PC cluster is also used by large numbers of people running Windows apps, and so this is not a solution for student access. Also many of our faculty are Mac users. The next most frequent suggestion was eXceed, from Hummingbird software (http://www.hcl.com/HOWTO.HTML). Positive experiences were reported by Fred Arnold (address above); Tom Pierce (rs0thp@rohmhaas.com), who used it specifically to access SPARTAN and MacroModel; and Ned Martin (martinn@uncwil.edu), accessing SPARTAN. eXceed also was mentioned in a very helpful summary from the CUR list provided by Mark Timken (timken@science.widener.edu). I have ordered a trial copy. MacX was the only software mentioned for Macintoshes, with positive experiences reported by Stephen Bowlus (BOWLUS@sandoz.com), Per Arvidsson (arvid@oc.chalmers.se), Dave Young (young@slater.cem.msu.edu), and Craig Burkhart (cburkhart@goodyear.com). We have some small experience with MacX ourselves, and find it usable, although a bit clunky. Other clients receiving some comment were XVision 6.0, used by Andrey Bliznyuk (Andrey.Bliznyuk@anu.edu.au) to access SPARTAN, but found poor by Tom Pierce (address above); ReflectionX (Stephen Bowlus; address above); the X-win32 shareware client suggested by Carlo Nervi, which Jim Macmillan (macmillan@cobra.uni.edu) found of poor quality. From an ad in BYTE, I had learned of XoftWare for Windows, from AGE Status: R Logic, Inc. (sales@age.com). Katie Breen was particularly helpful in faxing me a copy of the sales brochure. Xoftware comes in versions for both PC and Mac; Craig Martens (cmartens@uci.edu) has a positive experience with the Mac version. We will order trial copies. Similarly, we learned of PC Xware, from NCD, Inc. (info@pcx.ncd.com; http://www.ncd.com); no one seems to have had experience with this software, but from its literature it appears to be an especially robust application. It does not come in a Mac version, and is pricier than Xoftware. Several individuals suggested that accessing SPARTAN and other programs from more than 3-4 clients produced an unacceptable slowdown; Jim Macmillan suggested that the servers should be on their own branch of the local network to avoid untowrd effects on other users. Several respondants also reminded me that Wavefunction, supplier of SPARTAN, requires a $200 license for each client that accesses SPARTAN over a network. This charge is unfortunate; we will probably have to acquire licenses over several years to reach our full intended capacity. My thanks to all who responded, and apologies if I have inadvertantly omitted anyone's contribution. I will file a report later on our experiences with examination copies. Professor Ray Fort, Jr. Voice: (207)-581-1180 Department of Chemistry FAX: (207)-581-1191 University of Maine E-mail: rcfort@maine.maine.edu Orono ME 04469 rfortjr@fort.umeche.maine.edu Computational organic chemistry, especially on wood- and paper-related problems From /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com Mon Oct 30 13:51:25 1995 Received: from merit-mx1.telemail.net for /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com by www.ccl.net (8.6.10/950822.1) id NAA18938; Mon, 30 Oct 1995 13:51:23 -0500 From: X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Mon, 30 Oct 1995 11:30:00 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Mon, 30 Oct 1995 11:30:00 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Mon, 30 Oct 1995 11:30:00 -0500 X400-Received: by /PRMD=LANGATE/ADMD=TELEMAIL/C=GB/; Relayed; Mon, 30 Oct 1995 11:30:00 -0500 Date: Mon, 30 Oct 1995 11:30:00 -0500 X400-Originator: /G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/@LANGATE.gb.sprint.com X400-Recipients: non-disclosure:; X400-MTS-Identifier: [/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/;Mon Oct 30 11:30:12 199500] X400-Content-Type: P2-1984 (2) Content-Identifier: Re: CCL:MOPAC Er Message-ID: <"Mon Oct 30 11:30:12 199500*/G=Matthew/S=Harbowy/OU=LIPTONUS-EC02/O=TMUS.TJL/PRMD=LANGATE/ADMD=TELEMAIL/C=GB/"@MHS> To: chemistry@www.ccl.net Subject: Re: CCL:MOPAC Error Message. Posted-Date: Fri, 27 Oct 95 19:00:21 -0400 X-Mailer: Cem X11/Mailer Version 9.2mgm (Wed Jan 5 12:38:09 EST 1994) Content-Type: text Content-Length: 2299 Status: RO Errors-To: jkl@ccl.net Precedence: bulk The error meassage occurs because you have chosen seven orbitals for a c.i. calculation, and one of the two on the extrema of this selection is near-degenerate with one not selected. You either need to tell MOPAC how many filled orbitals you want (c.i.=7,n) where n is the number of filled orbitals, so that you select ones that are non-near-degenrate, or need to expand or reduce your c.i. Convergence isn't going to help you fix the error message: the problem may float in and out because the orbitals will move slightly with optimization. matt ______________________________ Reply Separator _________________________________ Subject: CCL:MOPAC Error Message. Author: chemistry-request@ccl.net at INTERNET Date: 10/29/95 2:10 AM Dear Net-surfers, I am attempting to use MOPAC 6.0 to construct Jablonski diagrams for several dyes, and for now I am interested in the singlet excited state energies. I am using the PM3 optimised structure (gradient approx.=1) as my input for several SCF energy calculations, to obtain excited state energies in which I used the following keywords (PM3): SINGLET C.I.=7 ROOT={n+1} Where n=1,2,3,4,5,6 For S1, S2, S3, respectively. Unfortunatly, in the case of several structures, MOPAC stopped and returned an error message, viz: `Degenerate energy levels detected in the MECI. Some of these levels would be treated by MECI, while others would not. This would lead to non-reproducable electronic energies. Job stopped; to continue specify GEO-OK." I added the keyword PRECISE to try and tighten the SCF convergence criteria, however, this seemed to have no effect. Reluctantly, I added the keyword GEO-OK and the energy levels were returned as expected, but....... * Could someone please tell me: a) What does the abovementioned error message really mean? Does it refer to M.O.s or states or something else in the C.I. calculation? b) How can I avoid generation of the message? c) What are the consequences of specifying GEO-OK? I have also come across the same scenario when dealing with excited state geometry optimizations in the past, and once again, the only way around them seemed to be to use GEO-OK. I am concerned that by using this keyword, I am forcing the calculation to continue to completion when something is inherently problematic in my structure. I intend to summarise my responses to this question and post it to the list, as I did before. Thank you, Jason. _______________________________________________________________________________ Jason Lye, | Dye Synthesis Research Group, | College Of Textiles, Box 8301, | "If we did'nt have any bones, North Carolina State University, | we would have to live in a bucket." Raleigh, N.C. 27695 - 8301 | | Ph: (919) 515-6615 | jlye@tx.ncsu.edu | _______________________________________________________________________________ --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search Web: http://www.ccl.net/chemistry.html --- From itsigeln@chem.ucsd.edu Mon Oct 30 17:05:40 1995 Received: from UCSD.EDU for itsigeln@chem.ucsd.edu by www.ccl.net (8.6.10/950822.1) id RAA25395; Mon, 30 Oct 1995 17:05:38 -0500 Received: from chem.chem.ucsd.edu (chem.ucsd.edu [132.239.68.1]) by UCSD.EDU (8.6.12/8.6.9) with SMTP id OAA21205 for ; Mon, 30 Oct 1995 14:05:37 -0800 Received: by chem.chem.ucsd.edu (5.51) id AA02142; Mon, 30 Oct 95 14:03:54 PST Received: by chemod0-enet.ucsd.edu (931110.SGI) id AA29148; Mon, 30 Oct 95 14:07:46 -0800 Date: Mon, 30 Oct 95 14:07:46 -0800 From: itsigeln@chem.ucsd.edu (Igor Tsigelny) Message-Id: <9510302207.AA29148@chemod0-enet.ucsd.edu> To: CHEMISTRY-REQUEST@www.ccl.net Status: RO This is the summary of the responses I got to my request about ATP, GTP charges distribution. Sorry for delay with this digest but I waited for more information. Thanks for help. ------------------- >From wriggers@london.ks.uiuc.edu Tue Oct 3 21:23:30 1995 Date: Tue, 3 Oct 95 23:18:42 -0500 Dear Dr. Tsigelny, We did calculations of ADP and ATP charges with the GAUSSIAN92 6-31G* basis set, Merz-Kollman/Singh algorithm. They should be accurate enough for typical molecular dynamics simulations. Please find the data below. Our manuscript is in preparation: @article{WRIG96, author={Willy Wriggers and Klaus Schulten}, title={Conformational Differences in {G}-actin: A molecular dynamics study}, year=1996, note={In preparation} } Please ask for a preprint in about a month, we would appreciate if you would quote us should you decide to use the data. Also, there is a new CHARMM nucleic acid forcefield coming out soon with parameters and charges for the nucleotides. The paper is: MacKerell Jr., A.D., Wiorkiewicz-Kuczera, J. and Karplus, M. An all-atom empirical energy function for the simulation of nucleic acids. J.Amer.Chem.Soc. In Press. Best regards, Willy Wriggers _______________________________________________ wriggers@uiuc.edu (NeXT-mail OK) Willy R. Wriggers Theoretical Biophysics Group Beckman Institute University of Illinois at Urbana-Champaign 405 North Mathews Avenue Urbana, IL 61801, USA Telephone (217) 244-1612 Telefax (217) 244-6078 WorldWideWeb: http://www.ks.uiuc.edu/~wriggers/ ----------_______________________________________________ Below Dr. Wriggers gave the GAUSSIAN 92 results that, I think, have not to be spreaded on the net bulkly, because these are unpublished yet and even if these will be published most probably only the short part of them can be included in the paper. So I propose to CCL members that are interested in these results ask directly the authors about them. Igor Tsigelny's comment ____________________________________________________________ >From edvard@atf1.fagmed.uit.no Wed Oct 4 01:34:59 1995 Hi! I suggest you take a look at the update on the AMBER force field from the Kollman group at UCSF. They have published electrostatic potential based charges of building blocks which may be used to generate the molecules you have in mind. Reference: Cornell et al. (1995) JACS, 117:5179-5197. -oed. School of Medicine | Dept. of Pharmacology, IMB | TelePhone: +47 77 64 53 42 University of Tromsoe | TeleFax: +47 77 64 53 10 MH, Breivika | Email: edvard@fagmed.uit.no N-9037 TROMSOE, NORWAY | URL: http://atf1.fagmed.uit.no/mgl.html ------------------------------------------------------------------------------ >From edgecm@hau407.uk.sb.com Thu Oct 5 07:55:38 1995 Hi Igor, We have some data on GDP and GTP. It's published in J Mol. Mod., Tim Clark's electronic journal on http://www.organik.uni-erlangen.de See you, Colin >From yurel@stamail1.vut.EDU.AU Wed Oct 4 19:32:19 1995 Dear Igor, the very recent paper by of P.A. Kollman et al. in JACS 117, 5179 is probably something you are looking for. The previos most fundamental work was J.Comp.Chem. 7, 230. Or simply get charges from AMBER force field. * Elizabeth Yuriev Tel: 61 (3) 365 2217 * * Department of Environmental Management Fax: 61 (3) 365 2465 * * Victoria University of Technology s9230022@cougar.vut.edu.au * * PO Box 14428, MCMC, Melbourne yurel@stamail1.vut.edu.au * * Victoria 8001 Australia * ************************************************************************ ------------------------------------------------ IGOR TSIGELNY Ph.D. University of California, San Diego itsigeln@ucsd.edu From uucp@fti.udmurtia.su Wed Nov 1 01:31:22 1995 Received: from gw.mark-itt.ru for uucp@fti.udmurtia.su by www.ccl.net (8.6.10/950822.1) id BAA29109; Wed, 1 Nov 1995 01:17:04 -0500 Received: from fti.UUCP by gw.mark-itt.ru with UUCP id AA07733 (5.65/MARK-ITT for chemistry@www.ccl.net); Wed, 1 Nov 1995 10:15:25 +0400 Received: by fti.udmurtia.su (UUPC/@ v6.07alpha, 08Mar94) with UUCP; Wed, 1 Nov 1995 10:51:15 +0400 To: chemistry@www.ccl.net Message-Id: From: uufti@fti.udmurtia.su (Postmaster) Date: Wed, 1 Nov 95 10:51:14 +0400 (MSK) Return-Receipt-To: uufti@fti.udmurtia.su Organization: Physical-Technical Institute X-Mailer: dMail (Demos Mail v1.14a) Return-Receipt-To: uufti@fti.udmurtia.su Subject: CCL: grain size and microstrain calc. from XRD Lines: 23 Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Content-Length: 731 Status: R Dear CCL Netters, We are studying the mechanical alloying of the individual elements (transition metals in particular) by the Mossbauer and X-ray diffraction technique. The grain sizes and microstrain are very important for us. We are requesting a program that will allow us of calculating the grain size and internal strain from analysis of the X-ray peak shapes. Program must execute the corrections for K_alpha2 and instrumental broadening. We prefer that the program to be free. Thank you for your help. Sincerely, Gennady Dorofeev --------- Dr. G.A.Dorofeev Physico-Technical Institute Ural's Branch Russian Academy of Sciences Kirov St. 132 426001 Izhevsk RUSSIA E-mail: uufti@fti.udmurtia.su From mcblimts@leonis.nus.sg Fri Nov 3 19:45:48 1995 Received: from sable.nus.sg for mcblimts@leonis.nus.sg by www.ccl.net (8.6.10/950822.1) id TAA03016; Fri, 3 Nov 1995 19:43:28 -0500 Received: from leonis.nus.sg (root@leonis.nus.sg [137.132.1.18]) by sable.nus.sg (8.6.10/8.6.9) with ESMTP id IAA22897; Sat, 4 Nov 1995 08:41:43 +0800 Received: from ([137.132.42.122]) by leonis.nus.sg (8.6.10/8.6.9/CNS-3.5) with SMTP id IAA29485; Sat, 4 Nov 1995 08:41:41 +0800 Date: Sat, 4 Nov 1995 08:41:41 +0800 Message-Id: <199511040041.IAA29485@leonis.nus.sg> X-Sender: mcblimts@leonis.nus.sg To: chemistry@www.ccl.net From: mcblimts@leonis.nus.sg (Lim Teck Sin) Subject: phi,psi computation - a summary Cc: raghu@iss.nus.sg, rvis@iss.nus.sg, wlawton@iss.nus.sg, tim@iss.nus.sg, mcblab43@leonis.nus.sg, mcbgane@leonis.nus.sg, MORALEGA%A1@LLDMPC Hi, I received the following replies about phi,psi computation. Thanks! ----------------------------------------------------------------------- From: istvan@bioorg.ee.cua.edu Date: Wed, 1 Nov 1995 18:32:12 -0500 CHARMM is able to compute phi, psi angles of peptide backbones. Hope this will help, Istvan Date: Thu, 2 Nov 1995 11:07:21 +1100 From: Tracy Nero There should be a program to calculate these angles deposited in the PDB databank, they have a number of small programs to calculate various parameters/extract information. In case you don't have the PDB address anonymous ftp site pdb.pdb.bnl.gov gopher site pdb.pdb.bnl.gov:70 WWW site http://www.pdb.bnl.gov/ Cheers Tracy Nero tracy@austin.unimelb.edu.au Date: Thu, 2 Nov 1995 09:37:03 -0500 From: swamy@kgn.ibm.com (Swamy Kandadai) The pdb has a program for computing the phi and psi angles from the xyz coordinates in the pdb format. Thanks Swamy Kandadai From: cbas25 Date: Wed, 1 Nov 1995 20:37:36 +0000 (GMT) The program INTERCHEM will compute values of phi and psi given protein structures in a native format which can easily be derived from the pdb format using a tool called PROTEINS. Both programs are available from QCPE. Yours sincerely, Peter Bladon From: cbas25 Subject: Re: QCPE Date: Thu, 2 Nov 1995 10:06:00 +0000 (GMT) QCPE is the abrreviation for:- Quantum Chemistry Program Exchange Creative Arts Building 181 Indiana University Bloomington, IN 47405 USA Phone +1 812 855 4784 Fax +1 812 855 5539 email qcpe@ucs.indiana.edu The person in charge is Dr. Richard Counts QCPE holds copies of many programs (notably MOPAC) and distributes them at minimal costs. The INTERCHEM suite of programs costs $3000 for a non-academic license or $600 for an academic license. More information on INTERCHEM can be got from the world-wide web-page:- http://interchem.chem.strath.ac.uk/inter/interprobe.html I hope this helps Yours sincerely Date: Thu, 02 Nov 1995 08:36:29 -0600 From: Akbar Nayeem This is easily done in the Sybyl/Biopolymer module from Tripos. Akbar Nayeem Biopolymer Scientist Tripos Inc. From: David Wild Date: Thu, 2 Nov 1995 13:02:10 +0000 Hi there I've got hold of a fortran program from a guy called Mike Williamson at the molecular biology department here. I'm afraid I don't have any documentation for it, but I'll enclose it anyway. If you want to get in touch with him, his E-mail is M.Williamson@sheffield.ac.uk Best Wishes David Wild C Reads PDB file, works out phi and psi for all residues c Modification of phipsi.f for all chi c Modified again to give omega too. DIMENSION atom(8000),ires(8000),res(8000),x(8000) DIMENSION y(8000),z(8000),phi(800),psi(800),chi(800) DIMENSION seq(800),chi2(800),chi3(800),chi4(800) DIMENSION iphires(4,800),ipsires(4,800),ichires(4,800) DIMENSION ichi2res(4,800),ichi3res(4,800),omega(800) DIMENSION ichi4res(4,800),iomegares(4,800) CHARACTER FN1*40,line*80,res*3,atom*4,FN2*40,seq*3 COMMON x,y,z type *,'Input file?' accept 999,FN1 type *,'Output file?' accept 999,FN2 999 format(A) open(1,file=FN1,status='OLD') open(2,file=FN2) iatom=0 10 read(1,999)line if(line(1:4).eq.'END ') goto 100 if(line(1:4).ne.'ATOM') goto 10 iatom=iatom+1 read(line(13:16),'(A4)') atom(iatom) read(line(18:20),'(A3)') res(iatom) read(line(23:26),'(I4)') ires(iatom) c ires(iatom)=ires(iatom)-508 read(line(31:38),'(F8.3)') x(iatom) read(line(39:46),'(F8.3)') y(iatom) read(line(47:54),'(F8.3)') z(iatom) goto 10 100 continue write(2,998)ires(iatom),FN1 998 format(1X,I4,' residues detected for ',A) write(2,995) 995 format('NB The omega angle is for the bond AFTER ther residue') write(2,997) 997 format 1(' Residue Omega Phi Psi Chi1 Chi2 Chi3 Chi4 2') C locate line numbers for phi and psi calculation do 20 I=1,iatom if(atom(I).eq.' N ') then iomegares(3,ires(i)-1)=i iphires(2,ires(i))=i ipsires(1,ires(i))=i ipsires(4,ires(i)-1)=i ichires(1,ires(i))=i endif if(atom(i).eq.' CA ') then iomegares(1,ires(i))=i iomegares(4,ires(i)-1)=i iphires(3,ires(i))=i ipsires(2,ires(i))=i ichires(2,ires(i))=i ichi2res(1,ires(i))=i seq(ires(i))=res(i) endif if(atom(i).eq.' C ') then iomegares(2,ires(i))=i iphires(4,ires(i))=i iphires(1,ires(i)+1)=i ipsires(3,ires(i))=i endif if(atom(i).eq.' CB ') then ichires(3,ires(i))=i ichi2res(2,ires(i))=i ichi3res(1,ires(i))=i endif if(atom(i)(3:3).eq.'G') then if(res(i).eq.'ILE'.and.atom(i).eq.' CG2') goto 20 if(res(i).eq.'THR'.and.atom(i).eq.' CG2') goto 20 if(res(i).eq.'VAL'.and.atom(i).eq.' CG2') goto 20 ichires(4,ires(i))=i ichi2res(3,ires(i))=i ichi3res(2,ires(i))=i ichi4res(1,ires(i))=i endif if(atom(i)(3:3).eq.'D') then if(atom(i)(4:4).eq.'2') goto 20 ichi2res(4,ires(i))=i ichi3res(3,ires(i))=i ichi4res(2,ires(i))=i endif if(atom(i)(3:3).eq.'E') then if(atom(i)(4:4).eq.'2') goto 20 if(res(i).eq.'PHE') goto 20 if(res(i).eq.'TYR') goto 20 if(res(i).eq.'TRP') goto 20 if(res(i).eq.'HIS') goto 20 ichi3res(4,ires(i))=i ichi4res(3,ires(i))=i endif if(atom(i)(3:3).eq.'Z') then ichi4res(4,ires(i))=i endif 20 continue do 30 I=ires(1),ires(iatom) omega(i)=angle(iomegares(1,I),iomegares(2,I), 1 iomegares(3,I),iomegares(4,I)) phi(i)=angle(iphires(1,I),iphires(2,I),iphires(3,I), 1 iphires(4,I)) psi(i)=angle(ipsires(1,I),ipsires(2,I),ipsires(3,I), 1 ipsires(4,I)) chi(i)=angle(ichires(1,I),ichires(2,I),ichires(3,I), 1 ichires(4,I)) chi2(i)=angle(ichi2res(1,I),ichi2res(2,I), 1 ichi2res(3,I),ichi2res(4,I)) chi3(i)=angle(ichi3res(1,I),ichi3res(2,I), 1 ichi3res(3,I),ichi3res(4,I)) chi4(i)=angle(ichi4res(1,I),ichi4res(2,I), 1 ichi4res(3,I),ichi4res(4,I)) 30 continue do 40 I=ires(1),ires(iatom) write(2,996) I,seq(I),omega(I),phi(I),psi(I),chi(I), 1 chi2(I),chi3(I),chi4(I) 996 format(I5,1X,A3,1X,7F8.2) 40 continue stop end FUNCTION angle(i1,i2,i3,i4) C Gets line numbers i1 to i4, makes vectors i1-i2, i3-i4, C calculates vector and scalar products to get cos(angle) and C phi(angle), then angle DIMENSION x(8000),y(8000),z(8000) DIMENSION v21(3),v23(3),v34(3),v123(3),v234(3),v(3) COMMON x,y,z iresult=0 c if(x(i1).eq.0.0.or.x(i2).eq.0.0.or.x(i3).eq.0.0.or.x(i4). c 1 eq.0.0)iresult=1 if(i1.eq.0.or.i2.eq.0.or.i3.eq.0.or.i4.eq.0)iresult=1 v21(1)=x(i1)-x(i2) v21(2)=y(i1)-y(i2) v21(3)=z(i1)-z(i2) v23(1)=x(i3)-x(i2) v23(2)=y(i3)-y(i2) v23(3)=z(i3)-z(i2) v34(1)=x(i4)-x(i3) v34(2)=y(i4)-y(i3) v34(3)=z(i4)-z(i3) call vprod(v21,v23,v123,r1,st) call vprod(v23,v34,v234,r2,st) call vscal(v123,v234,scalp,cthet) call vprod(v123,v234,v,r3,sthet) call vscal(v,v23,scum,chet) if(chet.gt.0.0)chet=1.0 if(chet.lt.0.0)chet=-1.0 if(chet.eq.0.0) stop'CHET=0' angle=atan2((sthet*chet),cthet)*57.29578 angle=angle-180.0 if(angle.lt.-180.0)angle=angle+360.0 if(angle.gt.180.0)angle=angle-360.0 c if(iresult.eq.1)angle=-999.0 if(iresult.eq.1)angle=0 return end SUBROUTINE VPROD(a,b,p,r,sthet) DIMENSION a(3),b(3),p(3) P(1)=A(2)*B(3)-A(3)*B(2) P(2)=A(3)*B(1)-A(1)*B(3) P(3)=A(1)*B(2)-A(2)*B(1) R=SQRT(P(1)*P(1)+P(2)*P(2)+P(3)*P(3)) RA=SQRT(A(1)*A(1)+A(2)*A(2)+A(3)*A(3)) RB=SQRT(B(1)*B(1)+B(2)*B(2)+B(3)*B(3)) STHET=R/(RA*RB) RETURN END SUBROUTINE VSCAL(A,B,SC,THET) DIMENSION A(3),B(3) SC=A(1)*B(1)+A(2)*B(2)+A(3)*B(3) RA=SQRT(A(1)*A(1)+A(2)*A(2)+A(3)*A(3)) RB=SQRT(B(1)*B(1)+B(2)*B(2)+B(3)*B(3)) THET=SC/(RA*RB) RETURN END Dr David Wild, Department of Information Studies, University of Sheffield, Sheffield S10 2TN, U.K. Tel +44-(0)114 282 5093, Fax +44-(0)114 278 0300 Email D.J.Wild@sheffield.ac.uk http://www.shef.ac.uk/uni/academic/I-M/is/rstaff/ davewild.html ----------------------------------------------end of summary best regards - tecksin