From xavi@mompou.iqs.url.es Tue Jun 2 06:17:57 1998 Received: from mompou.iqs.url.es (mompou.iqs.url.es [193.145.86.4]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id GAA00265 Tue, 2 Jun 1998 06:17:47 -0400 (EDT) Received: by mompou.iqs.url.es (AIX 3.2/UCB 5.64/4.03) id AA21284; Tue, 2 Jun 1998 12:15:00 +0100 Date: Tue, 2 Jun 1998 12:14:59 +0100 (GDT) From: Xavi Corral To: chemistry@www.ccl.net Cc: Jordi_Teixido@RohmHaas.com Subject: PM3 Boron parameters Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers: I'm trying to find the PM3 parameters for the Boron atom. I'd be very thankful if someone has these parameters and could send them to me, or give me some references. I'll summarize. Thanks in advance, Carlos Bureu Delmas From takasima@indy.mol.rd.taisho.co.jp Tue Jun 2 07:03:46 1998 Received: from mail0.iij.ad.jp (mail0.iij.ad.jp [202.232.2.113]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id HAA00390 Tue, 2 Jun 1998 07:03:45 -0400 (EDT) Received: from uucp1.iij.ad.jp (uucp1.iij.ad.jp [202.232.2.201]) by mail0.iij.ad.jp (8.8.8/3.6W-MAIL) with SMTP id UAA21751 for ; Tue, 2 Jun 1998 20:03:40 +0900 (JST) Received: (from uucp@localhost) by uucp1.iij.ad.jp (8.6.12+2.4W/3.3W9-UUCP) with UUCP id UAA23314 for chemistry@www.ccl.net; Tue, 2 Jun 1998 20:03:40 +0900 Received: from sun02.mol.rd.taisho.co.jp (sun02.rd.taisho.co.jp [202.22.77.1]) by taisho.rd.taisho.co.jp (8.6.12+2.4W/3.4W2) with SMTP id UAA15934 for ; Tue, 2 Jun 1998 20:01:02 +0900 Received: from indy.mol.rd.taisho.co.jp by sun02.mol.rd.taisho.co.jp (4.1/6.4J.6-taisho) id AA19501; Tue, 2 Jun 98 19:57:14 JST Received: by indy.mol.rd.taisho.co.jp (940816.SGI.8.6.9/940406.SGI) id TAA15537; Tue, 2 Jun 1998 19:51:52 +0900 Date: Tue, 2 Jun 1998 19:51:52 +0900 From: takasima@indy.mol.rd.taisho.co.jp (Hajime Takashima) Message-Id: <199806021051.TAA15537@indy.mol.rd.taisho.co.jp> To: chemistry@www.ccl.net Subject: Bond order calculation in G94 Dear all, I am trying to execute the RHF calculation of a molecule (basis=365) in G94. I want to calculate the bond order and used the keyword AIM=BondOrders. But the following error message appeared. FATAL ERROR: DUPLICATE CRITICAL POINTS FOUND: 44 15 Error termination via Lnk1e in /usr/appli/g94/l609.exe. I would be glad to receive your suggestions. Sincerely, Hajime Takashima Molecular Science Lab. Medicinal Research Laboratories Taisho Pharmaceutical Co., Ltd. E-mail takasima@mol.rd.taisho.co.jp From shenkin@still3.chem.columbia.edu Tue Jun 2 10:51:48 1998 Received: from mailrelay1.cc.columbia.edu (cu41754@mailrelay1.cc.columbia.edu [128.59.35.143]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id KAA08038 Tue, 2 Jun 1998 10:51:48 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id KAA11276 for <@smtp.columbia.edu:CHEMISTRY@www.ccl.net>; Tue, 2 Jun 1998 10:51:41 -0400 (EDT) Received: by still3.chem.columbia.edu (950413.SGI.8.6.12/930416.SGI.AUTO) for CHEMISTRY@www.ccl.net id KAA18901; Tue, 2 Jun 1998 10:51:40 -0400 From: "Peter Shenkin" Message-Id: <9806021051.ZM18899@still3.chem.columbia.edu> Date: Tue, 2 Jun 1998 10:51:40 -0400 X-Mailer: Z-Mail (3.2.3 08feb96 MediaMail) To: CHEMISTRY@www.ccl.net Subject: mmio Version 67 now available in the CCL archives Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Mmio is a software libary containing C and Fortran procedures to read and write MacroModel structure files (i.e., the molecule description files that the MacroModel program uses; some other programs also read and/or write this format). The latest version has just been placed in: ftp://www.ccl.net/pub/chemistry/software/SOURCES/C/MacroModel-InpOut/ Compilation flags are provided for many platforms, but not all have been recently tested, so be careful. A slightly more detailed description is given in the file mmio_67.txt in the above directory, and fuller documentation is provided with the package. Mmio_67 is also available by descending through the "Updates and Freeware" link on the MacroModel home page. Enjoy, -P. -- *********** How can we have ethnic music without ethnic hatred? *********** * Peter S. Shenkin; Chemistry, Columbia U.; 3000 Broadway, Mail Code 3153 * ** NY, NY 10027; shenkin@columbia.edu; (212)854-5143; FAX: 678-9039 *** *MacroModel WWW page: http://www.columbia.edu/cu/chemistry/mmod/mmod.html * From sjardino@iq.usp.br Tue Jun 2 13:59:11 1998 Received: from quim.iq.usp.br (quim.iq.usp.br [143.107.46.101]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id NAA20190 Tue, 2 Jun 1998 13:59:08 -0400 (EDT) Received: (sjardino@localhost) by quim.iq.usp.br (8.6.10/SPARC10-IQ2.0) id OAA11599; Tue, 2 Jun 1998 14:50:10 -0300 Date: Tue, 2 Jun 1998 14:50:09 -0300 (EST) From: Sergio Augusto Jardino Filho To: chemistry@www.ccl.net Subject: Gaussian94 cbs-4 error In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, I have a problem with a CBS-4 method job of Gaussian94 that print the following message: Initial guess read from the checkpoint file: s20.chk Guess basis functions will be translated to current atomic coordinates. Logic error in ReDoC1: IndI= 312 but NBasI= 326. Error termination via Lnk1e in /usr/local/g94/l401.exe. Could someone help me? I would be very grateful Sergio A. Jardino Filho Universidade de Sao Paulo Instituto de Quimica From darrena@chem.leeds.ac.uk Tue Jun 2 14:14:39 1998 Received: from chemistry.leeds.ac.uk (chmsun1.leeds.ac.uk [129.11.12.1]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id OAA20337 Tue, 2 Jun 1998 14:14:38 -0400 (EDT) Received: from [129.11.12.138] (chmmac37.leeds.ac.uk [129.11.12.138]) by chemistry.leeds.ac.uk (8.8.8/8.8.8) with ESMTP id TAA24320 for ; Tue, 2 Jun 1998 19:14:33 +0100 (BST) Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Message-Id: Date: Tue, 2 Jun 1998 19:05:45 +0100 To: chemistry@www.ccl.net From: Darren Andrews Subject: GAMESS-US in parallel on NT Has anybody managed to make GAMESS run in parallel on a cluster of NT boxes? I've made a multiprocessor machine run GAMESS using shared memory, now I want to run it on about 12 Pentiums on an ethernet network. I would be very grateful if anyone can help. Cheers, Darren Andrews. PostGraduate Student, School of Chemistry, University of Leeds, Leeds. LS2 9JT. England. Darrena@chem.leeds.ac.uk Tel: 0113 233 6594. Fax: 0113 233 6565. From uucp@msi.com Tue Jun 2 07:29:48 1998 Received: from bioc1.msi.com (bioc1.msi.com [146.202.0.2]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with SMTP id HAA00508 Tue, 2 Jun 1998 07:29:47 -0400 (EDT) Received: by bioc1.msi.com (931110.SGI/930416.SGI) for CHEMISTRY@www.ccl.net id AA10785; Tue, 2 Jun 98 04:29:18 -0700 Received: from news.msi.com(146.202.0.224) by bioc1.msi.com via smap (V2.0) id xma010781; Tue, 2 Jun 98 04:29:14 -0700 Received: by news.msi.com (4.1/SMI-4.1) id AA19549; Tue, 2 Jun 98 04:19:54 PDT Newsgroups: msi.comp-chem-list Path: uucp From: Shyam Vyas Subject: Free Volumes in C2 X-Nntp-Posting-Host: 192.190.183.57 Content-Type: text/plain; charset=us-ascii Message-Id: <3573E1FC.6520B659@vishnu.msicam.co.uk> Sender: uucp@msi.com Content-Transfer-Encoding: 7bit Organization: Molecular Simulations Inc. References: <01BD8D36.420339E0.johnw@msi.com> Mime-Version: 1.0 Date: Tue, 2 Jun 1998 11:29:00 GMT X-Mailer: Mozilla 4.04 [en] (X11; I; IRIX 6.2 IP22) Apparently-To: CHEMISTRY@www.ccl.net Dear CCL'ers In reply to David De Vito's query, with regard to Free Volumes in Cerius2_3.5. The command efffectively calculates the total free volume, the occupiable volume (such as in the pore of a zeolite channel), and the accessible volume. The technique entails using a grid method and shares some similarities with the Access_Grid command in InsightII 400. The methods are very similar to the Connolly surface calculations, which are well documented in both the manuals and the literature. MSI would be happy to provide further information to its maintenance paying customers should they so wish. However, I'm sure as you all understand, it would be unfair to our maintenance paying customers if this information was freely available. Feel free to contact customer support if you have any further queries. Best regards, Shyam -- **************************** If you .. Dr. Shyam Vyas GRSC, DIC Support Scientist - Materials Science believe in nothing, Molecular Simulation love no one, 240/250 The Quorum and posses nothing Cambridge, CB5 8RE Email support@msicam.co.uk .. you will be happy. svyas@msicam.co.uk Phone +44 (0) 1223 413300 Fax +44 (0) 1223 413301 Hotline +44 (0) 345 413375 ***************************** From wtwinter@syr.edu Tue Jun 2 09:26:33 1998 Received: from mailer.syr.edu (mailer.syr.edu [128.230.20.20]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id JAA01728 Tue, 2 Jun 1998 09:26:32 -0400 (EDT) Received: from rodan.syr.edu by mailer.syr.edu (LSMTP for Windows NT v1.1a) with SMTP id <0.7B0464D0@mailer.syr.edu>; Tue, 2 Jun 1998 9:26:11 -0400 Received: from localhost (wtwinter@localhost) by rodan.syr.edu (8.8.7/8.8.7) with SMTP id JAA08871; Tue, 2 Jun 1998 09:26:09 -0400 (EDT) X-Authentication-Warning: rodan.syr.edu: wtwinter owned process doing -bs Date: Tue, 2 Jun 1998 09:26:09 -0400 (EDT) From: "William T. Winter" To: ccl Subject: Re: CCL:pdb file manipulator In-Reply-To: <3572B7AA.DB4A4E11@syr.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 1 Jun 1998, Igor J. Barani wrote: > I am looking for a pdb file manipulating software (preferably > shareware). Simply, I need to manipulate a large pdb file by performing > such operations as removing the hydrogens and adding dummy atoms etc. > Does anyone know where I can download a shareware program to do just > that? Thanks in advance for your responses. The MSI WebLab Viewer lite is freeware which does much of what you ask, it handles *.pdb, *.ent (hyperchem pdb files) and several other formats. It may be freely obtained from the following link http://www.msi.com/weblab/viewer/info/viewregisterlite.html =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Dr. William T. Winter, Director Phone: (315)470-6876 or 6586 Cellulose Research Institute FAX: (315)470-6856 SUNY-ESF, 121 E. C. Jahn Laboratory Internet: wtwinter@syr.edu Syracuse, NY 13210-2786 URL http://www-chem.esf.edu From yubofan@guomai.sh.cn Tue Jun 2 20:59:55 1998 Received: from guomai.sh.cn ([202.96.206.69]) by www.ccl.net (8.8.3/8.8.6/OSC/CCL 1.0) with ESMTP id UAA23235 Tue, 2 Jun 1998 20:59:49 -0400 (EDT) Received: from guomai.sh.cn (email-52 [210.0.0.52]) by guomai.sh.cn (8.8.8/8.8.8) with ESMTP id IAA26015 for ; Wed, 3 Jun 1998 08:56:28 +0900 (CDT) Message-ID: <35749F08.7DD4AA8@guomai.sh.cn> Date: Wed, 03 Jun 1998 08:55:39 +0800 From: Yubo Fan Reply-To: yubofan@guomai.sh.cn Organization: Department of Chemistry, Fudan University X-Mailer: Mozilla 4.04 [en] (Win95; I) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Summary: Cyclodextrin. References: <356CD065.E0DEA075@guomai.sh.cn> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi, everyone, I sent an email to ask the structures of cyclodextrin several days ago. Till now I have received many emails. Thanks a lot. > Hi, everyone, > > I have been looking for the structure of cyclodextrin in the Web but > failed. Is there cyclodextrin structure file (for example, PDB file) in > the InterNet? Or, if someone have, could you please send me one copy by > email? I need the structures of alpha-cyclodextrin, beta-cyclodextrin > and gamma-cyclodextrin. The precise structure data is preferred, for > instance, the data from monocrystal or by calculation. > > With best regards > > Y. Fan Dear Dr. Fan, please have a look at: http://caramel.oc.chemie.tu-darmstadt.de/~lemmi/molcad/cyc_iso1.html and ask Dr. Immel (at the bottom of the WWW-page) by e-mail for the structure data you need. Best regards from Stuttgart, Germany, Heinz Poehlmann .-------------------------------------------------------------------------. | Dr. Heinz W. Poehlmann Regionales Rechenzentrum | | Manager Applications Department der Universitaet Stuttgart | | Computational Chemistry Support (University Computer Center) | | phone: (49)-711-685-5992 RUS / HLRS | | fax: (49)-711-6787626 Allmandring 30 | | e-mail: poehlmann@hlrs.de D-70550 Stuttgart | | e-mail: poehlmann@rus.uni-stuttgart.de Germany | '-------------------------------------------------------------------------' Dear Yubo, have a look to our electronic poster page at: http://antas.agraria.uniss.it You'll find some papers on beta-cyclodextrin and you could download the pdb file bye Bruno Dr Bruno Manunza Molecular Modeling Lab DISAABA (Dept. of Agricultural Environm. Sci) University of Sassari V.le Italia 39 07100 Sassari, ITALY phone: 39 79 229215 fax: 39 79 229276 e-mail: bruno@antas.agraria.uniss.it web: http://antas.agraria.uniss.it Subject: Re: CCL:Cyclodextrin. Date: Thu, 28 May 1998 17:45:21 +0100 From: Peter Tebbutt To: yubofan@guomai.sh.cn Hi Yubo Fan, I know there is a structure of cyclodextrin shipped with the latest version of Chem3D Ultra (which we supply) but I don't expect you'd want to buy *just* for the structure, but you may be able to contact someone at CambridgeSoft and ask them where and how they got it. the web site is www.camsoft.com and all contacts are here. With regards Peter Tebbutt ChemSymphony Consultant Cherwell Scientific Publishing Subject: Date: Thu, 28 May 1998 22:38:38 -0400 From: "Genbin Shi" To: yubofan@guomai.sh.cn HETATM 2864 C11 BCD 371 -10.695 -3.048 2.018 1.00 44.16 1DMB2978 HETATM 2865 C21 BCD 371 -9.822 -2.557 0.835 1.00 41.96 1DMB2979 HETATM 2866 O21 BCD 371 -10.292 -3.169 -0.384 1.00 41.22 1DMB2980 HETATM 2867 C31 BCD 371 -8.347 -2.840 1.090 1.00 39.24 1DMB2981 HETATM 2868 O31 BCD 371 -7.539 -2.239 0.055 1.00 37.29 1DMB2982 HETATM 2869 C41 BCD 371 -7.919 -2.296 2.440 1.00 38.31 1DMB2983 HETATM 2870 O41 BCD 371 -6.611 -2.820 2.694 1.00 35.68 1DMB2984 HETATM 2871 C51 BCD 371 -8.844 -2.756 3.560 1.00 38.64 1DMB2985 HETATM 2872 O51 BCD 371 -10.233 -2.402 3.204 1.00 41.49 1DMB2986 HETATM 2873 C61 BCD 371 -8.606 -2.123 4.910 1.00 38.11 1DMB2987 HETATM 2874 O61 BCD 371 -9.468 -2.752 5.872 1.00 38.72 1DMB2988 HETATM 2875 C12 BCD 371 -5.613 -1.953 3.133 1.00 33.23 1DMB2989 HETATM 2876 C22 BCD 371 -4.333 -2.133 2.309 1.00 31.78 1DMB2990 HETATM 2877 O22 BCD 371 -4.676 -1.971 0.924 1.00 30.82 1DMB2991 HETATM 2878 C32 BCD 371 -3.686 -3.461 2.647 1.00 32.17 1DMB2992 HETATM 2879 O32 BCD 371 -2.455 -3.571 1.909 1.00 29.27 1DMB2993 HETATM 2880 C42 BCD 371 -3.395 -3.532 4.144 1.00 33.44 1DMB2994 HETATM 2881 O42 BCD 371 -2.841 -4.818 4.436 1.00 36.32 1DMB2995 HETATM 2882 C52 BCD 371 -4.686 -3.107 4.929 1.00 33.06 1DMB2996 HETATM 2883 O52 BCD 371 -5.344 -2.160 4.511 1.00 33.51 1DMB2997 HETATM 2884 C62 BCD 371 -4.549 -3.315 6.415 1.00 32.59 1DMB2998 HETATM 2885 O62 BCD 371 -5.883 -3.621 6.808 1.00 33.01 1DMB2999 HETATM 2886 C13 BCD 371 -1.517 -5.001 4.857 1.00 38.44 1DMB3000 HETATM 2887 C23 BCD 371 -0.932 -6.211 4.128 1.00 39.94 1DMB3001 HETATM 2888 O23 BCD 371 -1.137 -6.034 2.698 1.00 41.05 1DMB3002 HETATM 2889 C33 BCD 371 -1.625 -7.480 4.573 1.00 41.82 1DMB3003 HETATM 2890 O33 BCD 371 -1.047 -8.602 3.875 1.00 43.17 1DMB3004 HETATM 2891 C43 BCD 371 -1.553 -7.642 6.070 1.00 41.98 1DMB3005 HETATM 2892 O43 BCD 371 -2.369 -8.742 6.418 1.00 45.81 1DMB3006 HETATM 2893 C53 BCD 371 -2.142 -6.400 6.742 1.00 40.30 1DMB3007 HETATM 2894 O53 BCD 371 -1.493 -5.234 6.262 1.00 39.57 1DMB3008 HETATM 2895 C63 BCD 371 -1.916 -6.454 8.275 1.00 39.59 1DMB3009 HETATM 2896 O63 BCD 371 -2.099 -5.298 8.983 1.00 38.96 1DMB3010 HETATM 2897 C14 BCD 371 -1.964 -9.647 7.437 1.00 47.95 1DMB3011 HETATM 2898 C24 BCD 371 -1.402 -10.903 6.699 1.00 49.38 1DMB3012 HETATM 2899 O24 BCD 371 -0.248 -10.584 5.947 1.00 48.08 1DMB3013 HETATM 2900 C34 BCD 371 -2.519 -11.412 5.791 1.00 50.04 1DMB3014 HETATM 2901 O34 BCD 371 -2.054 -12.478 4.960 1.00 53.04 1DMB3015 HETATM 2902 C44 BCD 371 -3.690 -11.818 6.656 1.00 50.60 1DMB3016 HETATM 2903 O44 BCD 371 -4.781 -12.155 5.775 1.00 51.64 1DMB3017 HETATM 2904 C54 BCD 371 -4.138 -10.630 7.509 1.00 50.75 1DMB3018 HETATM 2905 O54 BCD 371 -3.073 -10.004 8.199 1.00 48.61 1DMB3019 HETATM 2906 C64 BCD 371 -5.102 -11.149 8.634 1.00 51.84 1DMB3020 HETATM 2907 O64 BCD 371 -5.390 -10.038 9.471 1.00 54.82 1DMB3021 HETATM 2908 C15 BCD 371 -5.419 -13.414 5.945 1.00 52.23 1DMB3022 HETATM 2909 C25 BCD 371 -5.707 -13.994 4.576 1.00 52.24 1DMB3023 HETATM 2910 O25 BCD 371 -4.546 -13.981 3.725 1.00 52.16 1DMB3024 HETATM 2911 C35 BCD 371 -6.800 -13.172 3.886 1.00 53.12 1DMB3025 HETATM 2912 O35 BCD 371 -7.171 -13.786 2.640 1.00 52.81 1DMB3026 HETATM 2913 C45 BCD 371 -8.010 -13.090 4.780 1.00 52.87 1DMB3027 HETATM 2914 O45 BCD 371 -8.930 -12.190 4.114 1.00 52.91 1DMB3028 HETATM 2915 C55 BCD 371 -7.665 -12.498 6.169 1.00 52.76 1DMB3029 HETATM 2916 O55 BCD 371 -6.571 -13.255 6.733 1.00 53.32 1DMB3030 HETATM 2917 C65 BCD 371 -8.818 -12.637 7.086 1.00 52.15 1DMB3031 HETATM 2918 O65 BCD 371 -8.706 -11.845 8.242 1.00 52.49 1DMB3032 HETATM 2919 C16 BCD 371 -10.304 -12.590 4.018 1.00 53.25 1DMB3033 HETATM 2920 C26 BCD 371 -10.713 -12.447 2.599 1.00 53.73 1DMB3034 HETATM 2921 O26 BCD 371 -9.633 -12.943 1.788 1.00 53.90 1DMB3035 HETATM 2922 C36 BCD 371 -10.959 -10.996 2.183 1.00 53.67 1DMB3036 HETATM 2923 O36 BCD 371 -11.798 -11.037 0.979 1.00 54.50 1DMB3037 HETATM 2924 C46 BCD 371 -11.608 -10.162 3.187 1.00 53.38 1DMB3038 HETATM 2925 O46 BCD 371 -11.342 -8.781 2.766 1.00 53.24 1DMB3039 HETATM 2926 C56 BCD 371 -11.029 -10.352 4.581 1.00 53.59 1DMB3040 HETATM 2927 O56 BCD 371 -11.092 -11.766 4.871 1.00 53.68 1DMB3041 HETATM 2928 C66 BCD 371 -11.772 -9.657 5.726 1.00 54.48 1DMB3042 HETATM 2929 O66 BCD 371 -12.379 -10.540 6.427 1.00 56.29 1DMB3043 HETATM 2930 C17 BCD 371 -12.461 -8.130 2.145 1.00 52.98 1DMB3044 HETATM 2931 C27 BCD 371 -12.023 -7.621 0.792 1.00 52.83 1DMB3045 HETATM 2932 O27 BCD 371 -11.276 -8.655 0.107 1.00 53.92 1DMB3046 HETATM 2933 C37 BCD 371 -11.132 -6.390 0.892 1.00 53.08 1DMB3047 HETATM 2934 O37 BCD 371 -11.049 -5.776 -0.411 1.00 54.19 1DMB3048 HETATM 2935 C47 BCD 371 -11.670 -5.344 1.883 1.00 52.00 1DMB3049 HETATM 2936 O47 BCD 371 -10.554 -4.443 2.051 1.00 48.88 1DMB3050 HETATM 2937 C57 BCD 371 -11.910 -6.045 3.225 1.00 53.05 1DMB3051 HETATM 2938 O57 BCD 371 -12.888 -7.112 3.002 1.00 53.07 1DMB3052 HETATM 2939 C67 BCD 371 -12.545 -5.111 4.255 1.00 54.33 1DMB3053 HETATM 2940 O67 BCD 371 -11.847 -5.338 5.480 1.00 56.68 1DMB3054 Subject: it is another BCD Date: Thu, 28 May 1998 22:40:42 -0400 From: "Genbin Shi" To: yubofan@guomai.sh.cn HETATM 5267 C11 BCD 701 58.178 14.795 3.335 1.00 70.57 C HETATM 5268 C21 BCD 701 59.711 14.744 3.251 1.00 70.08 C HETATM 5269 O21 BCD 701 60.151 13.491 2.753 1.00 68.12 O HETATM 5270 C31 BCD 701 60.339 14.990 4.620 1.00 71.70 C HETATM 5271 O31 BCD 701 61.755 15.064 4.481 1.00 73.17 O HETATM 5272 C41 BCD 701 59.815 16.281 5.272 1.00 71.24 C HETATM 5273 O41 BCD 701 60.198 16.268 6.675 1.00 67.96 O HETATM 5274 C51 BCD 701 58.268 16.381 5.170 1.00 72.03 C HETATM 5275 O51 BCD 701 57.787 16.067 3.839 1.00 71.27 O HETATM 5276 C61 BCD 701 57.775 17.786 5.469 1.00 72.02 C HETATM 5277 O61 BCD 701 58.010 18.136 6.824 1.00 74.16 O HETATM 5278 C12 BCD 701 61.002 17.304 7.183 1.00 65.43 C HETATM 5279 C22 BCD 701 62.303 16.715 7.743 1.00 64.11 C HETATM 5280 O22 BCD 701 62.961 15.950 6.747 1.00 64.84 O HETATM 5281 C32 BCD 701 62.026 15.822 8.959 1.00 64.20 C HETATM 5282 O32 BCD 701 63.264 15.411 9.536 1.00 60.82 O HETATM 5283 C42 BCD 701 61.159 16.553 10.010 1.00 64.64 C HETATM 5284 O42 BCD 701 60.726 15.611 11.028 1.00 63.48 O HETATM 5285 C52 BCD 701 59.923 17.174 9.327 1.00 63.39 C HETATM 5286 O52 BCD 701 60.332 18.010 8.219 1.00 65.37 O HETATM 5287 C62 BCD 701 59.051 18.028 10.244 1.00 59.96 C HETATM 5288 O62 BCD 701 59.720 19.214 10.658 1.00 58.04 O HETATM 5289 C13 BCD 701 60.690 16.082 12.351 1.00 65.83 C HETATM 5290 C23 BCD 701 61.969 15.702 13.079 1.00 67.15 C HETATM 5291 O23 BCD 701 63.086 16.197 12.360 1.00 68.24 O HETATM 5292 C33 BCD 701 62.087 14.178 13.217 1.00 69.41 C HETATM 5293 O33 BCD 701 63.160 13.859 14.098 1.00 68.93 O HETATM 5294 C43 BCD 701 60.814 13.531 13.761 1.00 69.78 C HETATM 5295 O43 BCD 701 60.891 12.112 13.473 1.00 65.43 O HETATM 5296 C53 BCD 701 59.517 14.130 13.145 1.00 70.39 C HETATM 5297 O53 BCD 701 59.581 15.574 13.063 1.00 67.09 O HETATM 5298 C63 BCD 701 58.297 13.825 14.005 1.00 69.56 C HETATM 5299 O63 BCD 701 58.447 14.365 15.314 1.00 63.90 O HETATM 5300 C14 BCD 701 60.650 11.225 14.532 1.00 63.03 C HETATM 5301 C24 BCD 701 61.481 9.940 14.337 1.00 61.25 C HETATM 5302 O24 BCD 701 62.825 10.281 14.008 1.00 61.24 O HETATM 5303 C34 BCD 701 60.894 9.060 13.226 1.00 60.24 C HETATM 5304 O34 BCD 701 61.553 7.801 13.188 1.00 58.92 O HETATM 5305 C44 BCD 701 59.400 8.835 13.433 1.00 61.38 C HETATM 5306 O44 BCD 701 58.884 8.110 12.299 1.00 65.50 O HETATM 5307 C54 BCD 701 58.705 10.193 13.549 1.00 61.65 C HETATM 5308 O54 BCD 701 59.261 10.922 14.665 1.00 62.66 O HETATM 5309 C64 BCD 701 57.191 10.117 13.744 1.00 59.06 C HETATM 5310 O64 BCD 701 56.834 9.148 14.716 1.00 59.30 O HETATM 5311 C15 BCD 701 58.093 6.985 12.557 1.00 66.61 C HETATM 5312 C25 BCD 701 58.378 5.937 11.494 1.00 66.33 C HETATM 5313 O25 BCD 701 59.777 5.668 11.448 1.00 65.04 O HETATM 5314 C35 BCD 701 57.905 6.447 10.136 1.00 64.90 C HETATM 5315 O35 BCD 701 58.126 5.438 9.166 1.00 62.58 O HETATM 5316 C45 BCD 701 56.412 6.823 10.173 1.00 68.60 C HETATM 5317 O45 BCD 701 56.049 7.474 8.925 1.00 73.83 O HETATM 5318 C55 BCD 701 56.132 7.790 11.345 1.00 68.27 C HETATM 5319 O55 BCD 701 56.697 7.293 12.589 1.00 69.34 O HETATM 5320 C65 BCD 701 54.634 8.002 11.595 1.00 66.79 C HETATM 5321 O65 BCD 701 54.354 8.289 12.964 1.00 60.09 O HETATM 5322 C16 BCD 701 54.996 6.930 8.158 1.00 77.25 C HETATM 5323 C26 BCD 701 55.545 6.380 6.840 1.00 79.46 C HETATM 5324 O26 BCD 701 56.534 5.392 7.086 1.00 82.77 O HETATM 5325 C36 BCD 701 56.144 7.523 6.021 1.00 79.00 C HETATM 5326 O36 BCD 701 56.677 7.014 4.802 1.00 77.18 O HETATM 5327 C46 BCD 701 55.077 8.608 5.743 1.00 76.30 C HETATM 5328 O46 BCD 701 55.728 9.771 5.155 1.00 75.01 O HETATM 5329 C56 BCD 701 54.389 9.039 7.068 1.00 77.02 C HETATM 5330 O56 BCD 701 53.973 7.892 7.871 1.00 78.19 O HETATM 5331 C66 BCD 701 53.145 9.914 6.844 1.00 76.48 C HETATM 5332 O66 BCD 701 52.042 9.170 6.330 1.00 69.20 O HETATM 5333 C17 BCD 701 55.301 10.241 3.896 1.00 74.81 C HETATM 5334 C27 BCD 701 56.498 10.316 2.945 1.00 75.34 C HETATM 5335 O27 BCD 701 57.195 9.075 2.953 1.00 75.29 O HETATM 5336 C37 BCD 701 57.462 11.438 3.354 1.00 73.43 C HETATM 5337 O37 BCD 701 58.477 11.566 2.370 1.00 71.99 O HETATM 5338 C47 BCD 701 56.748 12.786 3.516 1.00 72.74 C HETATM 5339 O47 BCD 701 57.678 13.733 4.123 1.00 71.60 O HETATM 5340 C57 BCD 701 55.496 12.622 4.414 1.00 72.45 C HETATM 5341 O57 BCD 701 54.659 11.519 3.969 1.00 74.88 O HETATM 5342 C67 BCD 701 54.606 13.862 4.421 1.00 72.56 C HETATM 5343 O67 BCD 701 53.899 14.008 3.192 1.00 68.22 O Ni hao, by seraching the PDB website at: http://www.pdb.bnl.gov/pdb-bin/pdbmain with the keyword "cyclodextrin" you will find the following entries: # 3DB database, Fri May 29 02:48:02 EDT 1998 # Query: kw=cyclodextrin&m=du # Hits: 16 (search time 0 sec) 1AC0 Glucoamylase, Granular Starch-Binding Doma... Sorimachi 1ACZ Glucoamylase, Granular Starch-Binding Doma... Sorimachi 1BTC Beta-Amylase with Alpha-Cyclodextrin (Alph... Mikami 2.00 1CDG Cyclodextrin Glycosyltransferase (Cgtase) Lawson 2.00 1CGT Cyclodextrin Glycosyltransferase Klein 2.00 1CGU Cyclodextrin Glycosyltransferase mutant As... Klein 2.50 1CIU Thermostable Cgtase From Thermoanaerobacte... Knegtel 2.30 1CXE Complex Of Cgtase With Maltotetraose At Ro... Knegtel 2.10 1CXF Complex Of A (D229n E257q) Double Mutant C... Knegtel 2.60 1CXH Complex Of Cgtase With Maltotetraose At Ro... Knegtel 2.40 1CXI Wild-Type Cgtase From Bacillus Circulans S... Knegtel 2.20 1CYG Cyclodextrin Glucanotransferase (Cgtase) Kubota 2.50 1DIJ Complex Of A Y195f Mutant Cgtase From B. C... Strokopytov 2.60 1PAM Cyclodextrin Glucanotransferase Harata 1.80 1TCM Cyclodextrin Glycosyltransferase W616a Mut... Knegtel 2.20 3CGT Structure Of Cyclodextrin Glycosyltransfer... Schmidt 2.40 Some of these structures are complexes of enzymes complexed with alpha and beta cyclodextrins. Small molecule structures in the PDB are usually less accurate than those in the CSD (which also contains several cyclo- dextrin structures) but unfortunately the CSD requires a license that you will have to pay for before you can access their structures. I hope this helps you out. Best regards, Ronald Knegtel ------------------------------------------------------------------------------- Dr. Ronald M. A. Knegtel Research Scientist Dept. of Molecular Design and Informatics Phone : +31-412-661469 N.V. Organon, RK2340 Fax : +31-412-662539 P.O. Box 20 5340 BH Oss http://www.organon.nl/ The Netherlands E-Mail : r.knegtel@organon.oss.akzonobel.nl ------------------------------------------------------------------------------- Subject: Alpha and Beta cyclodextrin PDB files Date: Tue, 02 Jun 1998 14:27:33 +0900 From: "Tomasz Girek" To: yubofan@guomai.sh.cn Dear Yubo, I have the pdb files of alpha and beta cyclodextrin and bellow I added it, but I am also looking for optimized ctruktures of all cyclodextrins. If somebody others sended to you this data, plesa send it to me I will be very obliged Sincerelly Yours Tom Tomasz Girek Ph.D. Graduate School of Biotechnology Korea University 5-1, Anam-dong, Sungbuk-ku 136-701 Seoul, Korea e-mail: girek@kuccnx.korea.ac.kr t.girek@wsp.czest.pl COMPND ACX ALPHA-CYCLODEXTRIN (CYCLOHEXA-AMYLOSE) REMARK ACX Extracted from PDB file 1cxf.pdb REMARK ACX Formula C36 H60 O30 REMARK ACX Nr of non-hydrogen atoms 66 REMARK ACX Residue type ACX REMARK ACX Residue name 90 REMARK ACX Original residue name (for O) $688 REMARK ACX RESOLUTION. 2.6 ANGSTROMS. 1CXF 61 REMARK ==> Deduced formula : (C 36 O 30) REMARK Est. total nr of hydrogens : ( 60) ATOM 1 C1A ACX 90 -4.386 2.634 0.411 1.00 20.00 ATOM 2 C2A ACX 90 -5.059 1.442 1.047 1.00 20.00 ATOM 3 C3A ACX 90 -4.501 0.157 0.497 1.00 20.00 ATOM 4 C4A ACX 90 -4.561 0.122 -1.008 1.00 20.00 ATOM 5 C5A ACX 90 -3.831 1.333 -1.522 1.00 20.00 ATOM 6 C6A ACX 90 -3.940 1.462 -3.002 1.00 20.00 ATOM 7 O1A ACX 90 -3.055 2.660 0.836 1.00 20.00 ATOM 8 O2A ACX 90 -4.853 1.490 2.447 1.00 20.00 ATOM 9 O3A ACX 90 -5.169 -0.993 1.009 1.00 20.00 ATOM 10 O5A ACX 90 -4.412 2.515 -0.994 1.00 20.00 ATOM 11 O6A ACX 90 -3.607 2.780 -3.427 1.00 20.00 ATOM 12 C1B ACX 90 -0.071 4.817 2.535 1.00 20.00 ATOM 13 C2B ACX 90 -1.239 4.524 3.431 1.00 20.00 ATOM 14 C3B ACX 90 -2.099 3.458 2.809 1.00 20.00 ATOM 15 C4B ACX 90 -2.495 3.844 1.408 1.00 20.00 ATOM 16 C5B ACX 90 -1.267 4.215 0.589 1.00 20.00 ATOM 17 C6B ACX 90 -1.651 4.848 -0.719 1.00 20.00 ATOM 18 O1B ACX 90 0.639 3.653 2.369 1.00 20.00 ATOM 19 O2B ACX 90 -0.805 4.060 4.712 1.00 20.00 ATOM 20 O3B ACX 90 -3.219 3.264 3.649 1.00 20.00 ATOM 21 O5B ACX 90 -0.576 5.243 1.281 1.00 20.00 ATOM 22 O6B ACX 90 -0.561 4.752 -1.631 1.00 20.00 ATOM 23 C1C ACX 90 4.327 1.923 2.339 1.00 20.00 ATOM 24 C2C ACX 90 3.748 2.112 3.726 1.00 20.00 ATOM 25 C3C ACX 90 2.271 2.414 3.602 1.00 20.00 ATOM 26 C4C ACX 90 2.019 3.598 2.691 1.00 20.00 ATOM 27 C5C ACX 90 2.779 3.489 1.372 1.00 20.00 ATOM 28 C6C ACX 90 2.856 4.808 0.666 1.00 20.00 ATOM 29 O1C ACX 90 3.664 0.842 1.714 1.00 20.00 ATOM 30 O2C ACX 90 3.993 0.955 4.523 1.00 20.00 ATOM 31 O3C ACX 90 1.676 2.740 4.857 1.00 20.00 ATOM 32 O5C ACX 90 4.141 3.124 1.595 1.00 20.00 ATOM 33 O6C ACX 90 4.025 5.547 1.034 1.00 20.00 ATOM 34 C1D ACX 90 4.218 -2.793 -0.163 1.00 20.00 ATOM 35 C2D ACX 90 4.301 -2.780 1.337 1.00 20.00 ATOM 36 C3D ACX 90 3.717 -1.510 1.903 1.00 20.00 ATOM 37 C4D ACX 90 4.430 -0.311 1.316 1.00 20.00 ATOM 38 C5D ACX 90 4.486 -0.346 -0.219 1.00 20.00 ATOM 39 C6D ACX 90 5.553 0.597 -0.719 1.00 20.00 ATOM 40 O1D ACX 90 2.910 -2.986 -0.570 1.00 20.00 ATOM 41 O2D ACX 90 3.574 -3.883 1.881 1.00 20.00 ATOM 42 O3D ACX 90 3.828 -1.559 3.323 1.00 20.00 ATOM 43 O5D ACX 90 4.864 -1.639 -0.726 1.00 20.00 ATOM 44 O6D ACX 90 6.412 0.935 0.379 1.00 20.00 ATOM 45 C1E ACX 90 -0.085 -4.865 -2.733 1.00 20.00 ATOM 46 C2E ACX 90 0.557 -5.689 -1.630 1.00 20.00 ATOM 47 C3E ACX 90 1.262 -4.773 -0.672 1.00 20.00 ATOM 48 C4E ACX 90 2.368 -4.020 -1.388 1.00 20.00 ATOM 49 C5E ACX 90 1.858 -3.338 -2.650 1.00 20.00 ATOM 50 C6E ACX 90 3.024 -3.036 -3.555 1.00 20.00 ATOM 51 O1E ACX 90 -1.030 -3.974 -2.156 1.00 20.00 ATOM 52 O2E ACX 90 -0.387 -6.487 -0.924 1.00 20.00 ATOM 53 O3E ACX 90 1.835 -5.535 0.393 1.00 20.00 ATOM 54 O5E ACX 90 0.942 -4.149 -3.423 1.00 20.00 ATOM 55 O6E ACX 90 2.685 -2.276 -4.727 1.00 20.00 ATOM 56 C1F ACX 90 -4.413 -1.748 -2.527 1.00 20.00 ATOM 57 C2F ACX 90 -4.662 -3.099 -1.975 1.00 20.00 ATOM 58 C3F ACX 90 -3.334 -3.690 -1.552 1.00 20.00 ATOM 59 C4F ACX 90 -2.354 -3.772 -2.726 1.00 20.00 ATOM 60 C5F ACX 90 -2.295 -2.433 -3.475 1.00 20.00 ATOM 61 C6F ACX 90 -1.686 -2.561 -4.850 1.00 20.00 ATOM 62 O1F ACX 90 -3.852 -0.992 -1.526 1.00 20.00 ATOM 63 O2F ACX 90 -5.498 -2.927 -0.837 1.00 20.00 ATOM 64 O3F ACX 90 -3.554 -4.929 -0.884 1.00 20.00 ATOM 65 O5F ACX 90 -3.594 -1.878 -3.686 1.00 20.00 ATOM 66 O6F ACX 90 -0.863 -1.413 -5.083 1.00 20.00 END COMPND BCD BETA-CYCLODEXTRIN REMARK BCD Extracted from PDB file 1dmb.pdb REMARK BCD Formula C42 H70 O35 REMARK BCD Nr of non-hydrogen atoms 77 REMARK BCD Residue type BCD REMARK BCD Residue name 180 REMARK BCD Original residue name (for O) $371 REMARK BCD RESOLUTION. 1.80 ANGSTROMS. 1DMB 32 REMARK ==> Deduced formula : (C 42 O 35) REMARK Est. total nr of hydrogens : ( 67) ATOM 1 C11 BCD 180 -3.833 4.636 -2.253 1.00 20.00 ATOM 2 C21 BCD 180 -2.960 5.127 -3.436 1.00 20.00 ATOM 3 O21 BCD 180 -3.430 4.515 -4.655 1.00 20.00 ATOM 4 C31 BCD 180 -1.485 4.844 -3.181 1.00 20.00 ATOM 5 O31 BCD 180 -0.677 5.445 -4.216 1.00 20.00 ATOM 6 C41 BCD 180 -1.057 5.388 -1.831 1.00 20.00 ATOM 7 O41 BCD 180 0.251 4.864 -1.577 1.00 20.00 ATOM 8 C51 BCD 180 -1.982 4.928 -0.711 1.00 20.00 ATOM 9 O51 BCD 180 -3.371 5.282 -1.067 1.00 20.00 ATOM 10 C61 BCD 180 -1.744 5.561 0.639 1.00 20.00 ATOM 11 O61 BCD 180 -2.606 4.932 1.601 1.00 20.00 ATOM 12 C12 BCD 180 1.249 5.731 -1.138 1.00 20.00 ATOM 13 C22 BCD 180 2.529 5.551 -1.962 1.00 20.00 ATOM 14 O22 BCD 180 2.186 5.713 -3.347 1.00 20.00 ATOM 15 C32 BCD 180 3.176 4.223 -1.624 1.00 20.00 ATOM 16 O32 BCD 180 4.407 4.113 -2.362 1.00 20.00 ATOM 17 C42 BCD 180 3.467 4.152 -0.127 1.00 20.00 ATOM 18 O42 BCD 180 4.021 2.866 0.165 1.00 20.00 ATOM 19 C52 BCD 180 2.176 4.577 0.658 1.00 20.00 ATOM 20 O52 BCD 180 1.518 5.524 0.240 1.00 20.00 ATOM 21 C62 BCD 180 2.313 4.369 2.144 1.00 20.00 ATOM 22 O62 BCD 180 0.979 4.063 2.537 1.00 20.00 ATOM 23 C13 BCD 180 5.345 2.683 0.586 1.00 20.00 ATOM 24 C23 BCD 180 5.930 1.473 -0.143 1.00 20.00 ATOM 25 O23 BCD 180 5.725 1.650 -1.573 1.00 20.00 ATOM 26 C33 BCD 180 5.237 0.204 0.302 1.00 20.00 ATOM 27 O33 BCD 180 5.815 -0.918 -0.396 1.00 20.00 ATOM 28 C43 BCD 180 5.309 0.042 1.799 1.00 20.00 ATOM 29 O43 BCD 180 4.493 -1.058 2.147 1.00 20.00 ATOM 30 C53 BCD 180 4.720 1.284 2.471 1.00 20.00 ATOM 31 O53 BCD 180 5.369 2.450 1.991 1.00 20.00 ATOM 32 C63 BCD 180 4.946 1.230 4.004 1.00 20.00 ATOM 33 O63 BCD 180 4.763 2.386 4.712 1.00 20.00 ATOM 34 C14 BCD 180 4.898 -1.963 3.166 1.00 20.00 ATOM 35 C24 BCD 180 5.460 -3.219 2.428 1.00 20.00 ATOM 36 O24 BCD 180 6.614 -2.900 1.676 1.00 20.00 ATOM 37 C34 BCD 180 4.343 -3.728 1.520 1.00 20.00 ATOM 38 O34 BCD 180 4.808 -4.794 0.689 1.00 20.00 ATOM 39 C44 BCD 180 3.172 -4.134 2.385 1.00 20.00 ATOM 40 O44 BCD 180 2.081 -4.471 1.504 1.00 20.00 ATOM 41 C54 BCD 180 2.724 -2.946 3.238 1.00 20.00 ATOM 42 O54 BCD 180 3.789 -2.320 3.928 1.00 20.00 ATOM 43 C64 BCD 180 1.760 -3.465 4.363 1.00 20.00 ATOM 44 O64 BCD 180 1.472 -2.354 5.200 1.00 20.00 ATOM 45 C15 BCD 180 1.443 -5.730 1.674 1.00 20.00 ATOM 46 C25 BCD 180 1.155 -6.310 0.305 1.00 20.00 ATOM 47 O25 BCD 180 2.316 -6.297 -0.546 1.00 20.00 ATOM 48 C35 BCD 180 0.062 -5.488 -0.385 1.00 20.00 ATOM 49 O35 BCD 180 -0.309 -6.102 -1.631 1.00 20.00 ATOM 50 C45 BCD 180 -1.148 -5.406 0.509 1.00 20.00 ATOM 51 O45 BCD 180 -2.068 -4.506 -0.157 1.00 20.00 ATOM 52 C55 BCD 180 -0.803 -4.814 1.898 1.00 20.00 ATOM 53 O55 BCD 180 0.291 -5.571 2.462 1.00 20.00 ATOM 54 C65 BCD 180 -1.956 -4.953 2.815 1.00 20.00 ATOM 55 O65 BCD 180 -1.844 -4.161 3.971 1.00 20.00 ATOM 56 C16 BCD 180 -3.442 -4.906 -0.253 1.00 20.00 ATOM 57 C26 BCD 180 -3.851 -4.763 -1.672 1.00 20.00 ATOM 58 O26 BCD 180 -2.771 -5.259 -2.483 1.00 20.00 ATOM 59 C36 BCD 180 -4.097 -3.312 -2.088 1.00 20.00 ATOM 60 O36 BCD 180 -4.936 -3.353 -3.292 1.00 20.00 ATOM 61 C46 BCD 180 -4.746 -2.478 -1.084 1.00 20.00 ATOM 62 O46 BCD 180 -4.480 -1.097 -1.505 1.00 20.00 ATOM 63 C56 BCD 180 -4.167 -2.668 0.310 1.00 20.00 ATOM 64 O56 BCD 180 -4.230 -4.082 0.600 1.00 20.00 ATOM 65 C66 BCD 180 -4.910 -1.973 1.455 1.00 20.00 ATOM 66 O66 BCD 180 -5.517 -2.856 2.156 1.00 20.00 ATOM 67 C17 BCD 180 -5.599 -0.446 -2.126 1.00 20.00 ATOM 68 C27 BCD 180 -5.161 0.063 -3.479 1.00 20.00 ATOM 69 O27 BCD 180 -4.414 -0.971 -4.164 1.00 20.00 ATOM 70 C37 BCD 180 -4.270 1.294 -3.379 1.00 20.00 ATOM 71 O37 BCD 180 -4.187 1.908 -4.682 1.00 20.00 ATOM 72 C47 BCD 180 -4.808 2.340 -2.388 1.00 20.00 ATOM 73 O47 BCD 180 -3.692 3.241 -2.220 1.00 20.00 ATOM 74 C57 BCD 180 -5.048 1.639 -1.046 1.00 20.00 ATOM 75 O57 BCD 180 -6.026 0.572 -1.269 1.00 20.00 ATOM 76 C67 BCD 180 -5.683 2.573 -0.016 1.00 20.00 ATOM 77 O67 BCD 180 -4.985 2.346 1.209 1.00 20.00 END Here, I attached the beta-cyclodextrin file from Chem3D software. I have changed its original file format into PDB format. COMPND BCycloDextrin.PDB HETATM 1 C -5.934 0.982 0.623 HETATM 2 C -6.300 2.170 -0.263 HETATM 3 C -5.060 3.036 -0.531 HETATM 4 C -4.409 3.416 0.802 HETATM 5 C -4.073 2.163 1.609 HETATM 6 C -3.623 2.541 3.027 HETATM 7 C -4.444 -3.915 -0.833 HETATM 8 C -5.281 -3.160 -1.803 HETATM 9 C -5.136 -1.645 -1.627 HETATM 10 C -5.331 -1.271 -0.219 HETATM 11 C -4.366 -2.054 0.670 HETATM 12 C -4.418 -1.785 2.175 HETATM 13 C 0.332 -6.035 -1.594 HETATM 14 C -0.446 -5.768 -2.864 HETATM 15 C -1.403 -4.598 -2.614 HETATM 16 C -2.278 -4.939 -1.435 HETATM 17 C -1.459 -5.288 -0.183 HETATM 18 C -2.282 -5.832 0.918 HETATM 19 C 4.882 -3.634 -0.274 HETATM 20 C 4.791 -4.391 -1.617 HETATM 21 C 3.330 -4.446 -2.035 HETATM 22 C 2.502 -5.070 -0.938 HETATM 23 C 2.732 -4.349 0.388 HETATM 24 C 2.075 -5.133 1.565 HETATM 25 C 5.641 1.615 0.117 HETATM 26 C 6.072 0.913 -1.172 HETATM 27 C 5.213 -0.304 -1.440 HETATM 28 C 5.267 -1.229 -0.248 HETATM 29 C 4.823 -0.463 0.986 HETATM 30 C 4.900 -1.294 2.290 HETATM 31 C 2.224 5.651 0.597 HETATM 32 C 3.126 5.587 -0.641 HETATM 33 C 3.461 4.137 -0.957 HETATM 34 C 4.100 3.497 0.257 HETATM 35 C 3.153 3.598 1.457 HETATM 36 C 3.746 3.079 2.755 HETATM 37 C -3.054 5.422 0.908 HETATM 38 C -2.463 6.238 -0.248 HETATM 39 C -1.064 5.726 -0.600 HETATM 40 C -0.200 5.729 0.647 HETATM 41 C -0.851 4.995 1.816 HETATM 42 C -0.133 5.227 3.137 HETATM 43 O -6.861 1.696 -1.487 HETATM 44 O -5.451 4.239 -1.200 HETATM 45 O -3.184 4.087 0.450 HETATM 46 O -5.322 1.425 1.814 HETATM 47 O -3.193 1.377 3.682 HETATM 48 O -4.907 -3.550 -3.139 HETATM 49 O -6.100 -0.978 -2.494 HETATM 50 O -5.040 0.148 -0.112 HETATM 51 O -4.722 -3.453 0.442 HETATM 52 O -3.443 -2.320 2.766 HETATM 53 O -5.507 -1.857 2.936 HETATM 54 O 0.435 -5.478 -3.957 HETATM 55 O -2.243 -4.389 -3.758 HETATM 56 O -3.063 -3.738 -1.181 HETATM 57 O -0.525 -6.343 -0.529 HETATM 58 O -2.992 -6.912 0.486 HETATM 59 O 5.564 -3.729 -2.616 HETATM 60 O 3.188 -5.200 -3.252 HETATM 61 O 1.118 -4.889 -1.315 HETATM 62 O 4.117 -4.290 0.689 HETATM 63 O 2.203 -4.410 2.763 HETATM 64 O 6.012 1.858 -2.266 HETATM 65 O 5.682 -0.961 -2.618 HETATM 66 O 4.393 -2.312 -0.494 HETATM 67 O 5.660 0.689 1.200 HETATM 68 O 6.136 -1.912 2.471 HETATM 69 O 2.411 6.229 -1.730 HETATM 70 O 4.377 4.100 -2.070 HETATM 71 O 4.326 2.119 -0.069 HETATM 72 O 2.877 5.006 1.686 HETATM 73 O 4.958 3.730 3.114 HETATM 74 O -3.325 6.164 -1.400 HETATM 75 O -0.468 6.571 -1.602 HETATM 76 O 0.993 5.034 0.302 HETATM 77 O -2.210 5.507 2.031 HETATM 78 O -0.112 6.625 3.432 HETATM 79 H -6.858 0.446 0.920 HETATM 80 H -7.075 2.783 0.243 HETATM 81 H -4.335 2.461 -1.145 HETATM 82 H -5.107 4.054 1.386 HETATM 83 H -3.258 1.604 1.100 HETATM 84 H -4.492 2.928 3.600 HETATM 85 H -2.743 3.217 2.967 HETATM 86 H -4.732 -4.986 -0.854 HETATM 87 H -6.346 -3.446 -1.672 HETATM 88 H -4.122 -1.330 -1.955 HETATM 89 H -6.377 -1.498 0.082 HETATM 90 H -3.324 -1.878 0.327 HETATM 91 H 0.986 -6.918 -1.742 HETATM 92 H -1.033 -6.672 -3.135 HETATM 93 H -0.815 -3.683 -2.384 HETATM 94 H -2.933 -5.797 -1.698 HETATM 95 H -0.922 -4.382 0.171 HETATM 96 H -3.024 -5.069 1.237 HETATM 97 H -1.617 -6.192 1.732 HETATM 98 H 5.931 -3.651 0.087 HETATM 99 H 5.177 -5.424 -1.486 HETATM 100 H 2.964 -3.417 -2.234 HETATM 101 H 2.779 -6.141 -0.829 HETATM 102 H 2.294 -3.330 0.335 HETATM 103 H 2.612 -6.095 1.714 HETATM 104 H 0.986 -5.243 1.373 HETATM 105 H 6.372 2.411 0.366 HETATM 106 H 7.135 0.602 -1.084 HETATM 107 H 4.163 0.016 -1.611 HETATM 108 H 6.309 -1.587 -0.105 HETATM 109 H 3.782 -0.100 0.841 HETATM 110 H 4.140 -2.103 2.257 HETATM 111 H 4.747 -0.625 3.163 HETATM 112 H 2.080 6.710 0.893 HETATM 113 H 4.065 6.148 -0.442 HETATM 114 H 2.529 3.590 -1.214 HETATM 115 H 5.051 4.021 0.492 HETATM 116 H 2.214 3.046 1.234 HETATM 117 H 3.984 2.000 2.647 HETATM 118 H 3.030 3.257 3.586 HETATM 119 H -4.079 5.784 1.128 HETATM 120 H -2.400 7.307 0.049 HETATM 121 H -1.139 4.690 -0.993 HETATM 122 H 0.015 6.778 0.944 HETATM 123 H -0.878 3.906 1.598 HETATM 124 H 0.926 4.905 3.043 HETATM 125 H -0.700 4.737 3.957 HETATM 126 H -7.072 2.455 -2.004 HETATM 127 H -4.666 4.739 -1.344 HETATM 128 H -2.923 1.634 4.547 HETATM 129 H -5.451 -3.058 -3.730 HETATM 130 H -5.989 -0.052 -2.366 HETATM 131 H -5.221 -1.634 3.838 HETATM 132 H -0.106 -5.322 -4.712 HETATM 133 H -2.808 -3.663 -3.554 HETATM 134 H -3.496 -7.220 1.220 HETATM 135 H 5.473 -4.229 -3.409 HETATM 136 H 2.270 -5.203 -3.466 HETATM 137 H 1.793 -4.923 3.438 HETATM 138 H 6.283 1.396 -3.042 HETATM 139 H 5.126 -1.710 -2.753 HETATM 140 H 6.088 -2.389 3.281 HETATM 141 H 2.970 6.187 -2.487 HETATM 142 H 4.564 3.193 -2.241 HETATM 143 H 5.247 3.345 3.923 HETATM 144 H -2.920 6.678 -2.079 HETATM 145 H 0.387 6.218 -1.784 HETATM 146 H 0.339 6.725 4.253 CONECT 1 2 46 50 79 CONECT 2 1 3 43 80 CONECT 3 2 4 44 81 CONECT 4 3 5 45 82 CONECT 5 4 6 46 83 CONECT 6 5 47 84 85 CONECT 7 8 51 56 86 CONECT 8 7 9 48 87 CONECT 9 8 10 49 88 CONECT 10 9 11 50 89 CONECT 11 10 12 51 90 CONECT 12 11 52 53 CONECT 13 14 57 61 91 CONECT 14 13 15 54 92 CONECT 15 14 16 55 93 CONECT 16 15 17 56 94 CONECT 17 16 18 57 95 CONECT 18 17 58 96 97 CONECT 19 20 62 66 98 CONECT 20 19 21 59 99 CONECT 21 20 22 60 100 CONECT 22 21 23 61 101 CONECT 23 22 24 62 102 CONECT 24 23 63 103 104 CONECT 25 26 67 71 105 CONECT 26 25 27 64 106 CONECT 27 26 28 65 107 CONECT 28 27 29 66 108 CONECT 29 28 30 67 109 CONECT 30 29 68 110 111 CONECT 31 32 72 76 112 CONECT 32 31 33 69 113 CONECT 33 32 34 70 114 CONECT 34 33 35 71 115 CONECT 35 34 36 72 116 CONECT 36 35 73 117 118 CONECT 37 38 45 77 119 CONECT 38 37 39 74 120 CONECT 39 38 40 75 121 CONECT 40 39 41 76 122 CONECT 41 40 42 77 123 CONECT 42 41 78 124 125 CONECT 43 2 126 CONECT 44 3 127 CONECT 45 4 37 CONECT 46 1 5 CONECT 47 6 128 CONECT 48 8 129 CONECT 49 9 130 CONECT 50 1 10 CONECT 51 7 11 CONECT 52 12 CONECT 53 12 131 CONECT 54 14 132 CONECT 55 15 133 CONECT 56 7 16 CONECT 57 13 17 CONECT 58 18 134 CONECT 59 20 135 CONECT 60 21 136 CONECT 61 13 22 CONECT 62 19 23 CONECT 63 24 137 CONECT 64 26 138 CONECT 65 27 139 CONECT 66 19 28 CONECT 67 25 29 CONECT 68 30 140 CONECT 69 32 141 CONECT 70 33 142 CONECT 71 25 34 CONECT 72 31 35 CONECT 73 36 143 CONECT 74 38 144 CONECT 75 39 145 CONECT 76 31 40 CONECT 77 37 41 CONECT 78 42 146 CONECT 79 1 CONECT 80 2 CONECT 81 3 CONECT 82 4 CONECT 83 5 CONECT 84 6 CONECT 85 6 CONECT 86 7 CONECT 87 8 CONECT 88 9 CONECT 89 10 CONECT 90 11 CONECT 91 13 CONECT 92 14 CONECT 93 15 CONECT 94 16 CONECT 95 17 CONECT 96 18 CONECT 97 18 CONECT 98 19 CONECT 99 20 CONECT 100 21 CONECT 101 22 CONECT 102 23 CONECT 103 24 CONECT 104 24 CONECT 105 25 CONECT 106 26 CONECT 107 27 CONECT 108 28 CONECT 109 29 CONECT 110 30 CONECT 111 30 CONECT 112 31 CONECT 113 32 CONECT 114 33 CONECT 115 34 CONECT 116 35 CONECT 117 36 CONECT 118 36 CONECT 119 37 CONECT 120 38 CONECT 121 39 CONECT 122 40 CONECT 123 41 CONECT 124 42 CONECT 125 42 CONECT 126 43 CONECT 127 44 CONECT 128 47 CONECT 129 48 CONECT 130 49 CONECT 131 53 CONECT 132 54 CONECT 133 55 CONECT 134 58 CONECT 135 59 CONECT 136 60 CONECT 137 63 CONECT 138 64 CONECT 139 65 CONECT 140 68 CONECT 141 69 CONECT 142 70 CONECT 143 73 CONECT 144 74 CONECT 145 75 CONECT 146 78 END -- ============================================================= Yubo Fan Email: yubofan@guomai.sh.cn Organic Synthesis Lab yubofan@fudan.edu.cn The Department of Chemistry Fudan University Phone: 8621-65648139 No. 220 Handan Road Fax: 8621-65641740 Shanghai, 200433 P. R. China =============================================================