From owner-chemistry@ccl.net Mon May 7 00:11:00 2007 From: "Sue L chsue2004_._yahoo.com" To: CCL Subject: CCL: Interplane Angle Message-Id: <-34198-070507000725-13647-UP1pVvE8MvjmwdYTJ91/VQ:-:server.ccl.net> X-Original-From: "Sue L" Date: Mon, 7 May 2007 00:07:22 -0400 Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] Hi, Does anyone know a program that can measure an interplane angle from calculated structures? Many thanks Sue From owner-chemistry@ccl.net Mon May 7 00:45:00 2007 From: "Kalju Kahn kalju^-^chem.ucsb.edu" To: CCL Subject: CCL:G: Geometry symmetrizer code or algorithm? Message-Id: <-34199-070507001344-15170-QQFa5sCvBUKYVunZphKTMA---server.ccl.net> X-Original-From: "Kalju Kahn" Date: Mon, 7 May 2007 00:13:40 -0400 Sent to CCL by: "Kalju Kahn" [kalju-x-chem.ucsb.edu] Hello, I am looking for a free program, algorithm examples, or pertinent literature for symmetrizing almost symmetric molecular structures in Cartesian coordinates. I am aware that several big programs (e.g. Gaussian, Maestro) have some built-in capabilities to symmetrize structures but I am looking for a freely available code. Thank you, Kalju From owner-chemistry@ccl.net Mon May 7 01:21:00 2007 From: "Yousef Sharifi ysharifi _ gmail.com" To: CCL Subject: CCL: Nano Clusters Message-Id: <-34200-070507011837-21651-ujIbpbi69bZM7tftf7yPQA!=!server.ccl.net> X-Original-From: "Yousef Sharifi" Date: Mon, 7 May 2007 01:18:34 -0400 Sent to CCL by: "Yousef Sharifi" [ysharifi|a|gmail.com] I need a program to create spherical clusters, is there any program to create clusters? Thanks From owner-chemistry@ccl.net Mon May 7 08:44:00 2007 From: "Sobia Ahsan Halim sobia_halim..yahoo.com" To: CCL Subject: CCL: Looking for ways of RMSD calculation on different docking softwares Message-Id: <-34201-070507040533-383-egZt7QSKu18nkgup2XZMNw|a|server.ccl.net> X-Original-From: "Sobia Ahsan Halim" Date: Mon, 7 May 2007 04:05:30 -0400 Sent to CCL by: "Sobia Ahsan Halim" [sobia_halim###yahoo.com] Dear All Hi. I am trying to redock compounds on the protein's active site.But I am facing so many problems. (1)I am working on MOE2006.08 and wants to calculate RMSD between the docked conformation of the ligand and the ligand in the complex structure of protein but I couldn't find any option to calculate RMSD. If anyone can tell me the best possible way to calculate RMSD on MOE2006.08 or SVL and can give me command to calculate RMSD on SVL, I will be deeply grateful. (2)I am also working on AutoDock Tools, I find least energy but very high RMSD or vice versa. What is the possible way to overcome this problem?. (3)Is there any posssibility to directly calculate RMSD between two ligands which are of different vectors on VMD?????.... (4)Is there any option to calculate RMSD on FlexiDock???... It will be highly appreciated if anyone can help me out.. Thanks in a million. From owner-chemistry@ccl.net Mon May 7 09:47:00 2007 From: "Rene Thomsen rt===molegro.com" To: CCL Subject: CCL: Molegro releases Molegro Virtual Docker 2007 v2.2 Message-Id: <-34202-070507093743-6558-ggSUbLwqKNnxTUQE7yTpPQ,server.ccl.net> X-Original-From: "Rene Thomsen" Date: Mon, 7 May 2007 09:37:38 -0400 Sent to CCL by: "Rene Thomsen" [rt(_)molegro.com] Aarhus, Denmark, May 7th, 2007 - Molegro is pleased to announce a new release of Molegro Virtual Docker, an integrated platform for predicting protein-ligand interactions available for Windows, Linux, and Mac OS X. Molegro Virtual Docker offers high-quality docking based on a novel optimization technique combined with a user interface experience focusing on usability and productivity. New features in version 2.2: * Similarity Docking for flexible ligand alignment and focused template docking * Data Analyzer (formerly named 'Regression Tool') for creating regression models (using neural networks or MLR), visualizing data, and performing feature selection * Structure randomizer (randomization of position, orientation, and torsional angles) * Docking from external data sources making it easier to setup and distribute large screening runs To download a trial version, please visit our company website at: http://www.molegro.com. For more information contact: Rene Thomsen, CEO Molegro Hoegh-Guldbergs Gade 10, Bldg. 1090 DK-8000 Aarhus Denmark E-mail: rt[#]molegro.com Phone: (+45) 89 42 31 65 About Molegro Molegro is a Danish company founded in 2005. Our company concentrates on developing high-performance drug discovery solutions leading to a faster drug-development process. Our goal is to provide scientifically superior products focusing on both state-of-the-art algorithms and an intuitive graphical user interface experience. From owner-chemistry@ccl.net Mon May 7 10:28:01 2007 From: "Atul Agarwal aagarwal_._achillion.com" To: CCL Subject: CCL: Looking for ways of RMSD calculation on different docking softwares Message-Id: <-34203-070507102639-28232-ohWL70m/3Suc6btpUelkKg ~ server.ccl.net> X-Original-From: "Atul Agarwal" Content-class: urn:content-classes:message Content-Type: multipart/mixed; boundary="----_=_NextPart_001_01C790AE.F79B4B03" Date: Mon, 7 May 2007 09:52:35 -0400 MIME-Version: 1.0 Sent to CCL by: "Atul Agarwal" [aagarwal:_:achillion.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C790AE.F79B4B03 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Sobia, Attached herein is the solution from CCG tech support. Cheers, Atul Agarwal Achillion Pharm 300 George St New Haven, CT 06511 -----Original Message----- > From: owner-chemistry a ccl.net [mailto:owner-chemistry a ccl.net]=20 Sent: Monday, May 07, 2007 4:06 AM To: Atul Agarwal Subject: CCL: Looking for ways of RMSD calculation on different docking softwares Sent to CCL by: "Sobia Ahsan Halim" [sobia_halim###yahoo.com] Dear All Hi. I am trying to redock compounds on the protein's active site.But I am facing so many problems. (1)I am working on MOE2006.08 and wants to calculate RMSD between the docked conformation of the ligand and the ligand in the complex structure of protein but I couldn't find any option to calculate RMSD. If anyone can tell me the best possible way to calculate RMSD on MOE2006.08 or SVL and can give me command to calculate RMSD on SVL, I will be deeply grateful. (2)I am also working on AutoDock Tools, I find least energy but very high RMSD or vice versa. What is the possible way to overcome this problem?. (3)Is there any posssibility to directly calculate RMSD between two ligands which are of different vectors on VMD?????.... (4)Is there any option to calculate RMSD on FlexiDock???... It will be highly appreciated if anyone can help me out.. Thanks in a million. -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------_=_NextPart_001_01C790AE.F79B4B03 Content-Type: message/rfc822 Content-Transfer-Encoding: 7bit X-MimeOLE: Produced By Microsoft Exchange V6.5 Received: from rover.achillion.com ([10.10.1.120]) by icarus.achillion.com with Microsoft SMTPSVC(5.0.2195.6713); Mon, 5 Feb 2007 15:02:35 -0500 MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="----_=_NextPart_002_01C74960.93E07F80" Received: from chemcomp.ca (smtp.chemcomp.com [209.226.194.167]) by rover.achillion.com (8.13.4/8.13.4/Debian-3sarge3) with ESMTP id l15F1TiC032750 for ; Mon, 5 Feb 2007 15:01:29 GMT Received: from [192.1.1.46] (firewall.chemcomp.com [209.226.194.162]) (authenticated) by chemcomp.ca (8.11.6/8.11.6) with ESMTP id l15K30u15745; Mon, 5 Feb 2007 15:03:00 -0500 Return-Path: X-OriginalArrivalTime: 05 Feb 2007 20:02:35.0706 (UTC) FILETIME=[944C39A0:01C74960] User-Agent: Thunderbird 1.5.0.8 (Windows/20061025) X-Scanned-By: CanIt (www . roaringpenguin . com) on 10.10.1.120 X-Spam-Score: 1.60 (*) [Hold at 5.00] ADDR_NUMS_AT_BIGSITE,J_CHICKENPOX_33,UPPERCASE_25_50 X-Canit-Stats-ID: 1592618 - 35daa6cd8232 X-Bayes-Prob: 0.0001 (Score 0) Content-class: urn:content-classes:message Subject: RMSd between two ligands Date: Mon, 5 Feb 2007 16:03:06 -0400 Message-ID: <45C78D7A.8040005 a chemcomp.com> X-MS-Has-Attach: yes X-MS-TNEF-Correlator: Thread-Topic: RMSd between two ligands Thread-Index: AcdJYJRRt9yNMsmxRQe1ZhLj4yckaw== > From: "Emilio Xavier Esposito" To: , "Atul Agarwal" This is a multi-part message in MIME format. ------_=_NextPart_002_01C74960.93E07F80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Atul I've attached an SVL script to calculate the RMSd between two ligand=20 chains in the MOE 3D window. *Using rms.svl* - Save the file 'rms.svl' in your ~/svl directory - Load the file 'rms.svl' using the MOE Command Window: svl> load 'rms.svl' - To calculate the RMS between 2 ligands, in the MOE Commands window = type: svl> rms[] - The results will be returned to the SVL Command Window Please feel free to contact me if you have any additional questions=20 regarding this script or MOE in general. All the best Emilio --=20 Emilio Xavier Esposito Applications Scientist Chemical Computing Group, Inc. Phone: 514.393.1055 emilio a chemcomp.com ~~~~~~~~~~~~~~~~~~~~~~~ Please join us for the MOE Workshop in *San Diego* Wednesday, March 14, 2007 1:00 - 5:00PM http://www.chemcomp.com/ssupport-workshop.htm Please make plans to attend the CCG Users Group Meeting (UGM) June 26 - 29, 2007 Hotel Godin Montreal, Canada ------_=_NextPart_002_01C74960.93E07F80 Content-Type: text/plain; name="rms.svl" Content-Transfer-Encoding: base64 Content-Description: rms.svl Content-Disposition: inline; filename="rms.svl" I3N2bA0KLy8Jcm1zLnN2bAkJY2FsY3VsYXRlcyB0aGUgUk1TIGJldHdlZW4gdHdvIGNoYWlucyAo YW5kIG9ubHkgdHdvKQ0KLy8NCi8vCTAxLWZlYi0yMDAzIChleGUpIENyZWF0ZWQNCi8vDQovLyBD T1BZUklHSFQgKEMpIDE5OTgtMjAwNyBDSEVNSUNBTCBDT01QVVRJTkcgR1JPVVAgSU5DLiAgQUxM IFJJR0hUUyBSRVNFUlZFRC4NCi8vDQovLyBQRVJNSVNTSU9OIFRPIFVTRSwgQ09QWSwgTU9ESUZZ IEFORCBESVNUUklCVVRFIFRISVMgU09GVFdBUkUgSVMgSEVSRUJZDQovLyBHUkFOVEVEIFBST1ZJ REVEIFRIQVQ6ICgxKSBVTk1PRElGSUVEIE9SIEZVTkNUSU9OQUxMWSBFUVVJVkFMRU5UIENPREUN Ci8vIERFUklWRUQgRlJPTSBUSElTIFNPRlRXQVJFIE1VU1QgQ09OVEFJTiBUSElTIE5PVElDRTsg KDIpIEFMTCBDT0RFIERFUklWRUQNCi8vIEZST00gVEhJUyBTT0ZUV0FSRSBNVVNUIEFDS05PV0xF REdFIFRIRSBBVVRIT1IoUykgQU5EIElOU1RJVFVUSU9OKFMpOyAoMykNCi8vIFRIRSBOQU1FUyBP RiBUSEUgQVVUSE9SKFMpIEFORCBJTlNUSVRVVElPTihTKSBOT1QgQkUgVVNFRCBJTiBBRFZFUlRJ U0lORw0KLy8gT1IgUFVCTElDSVRZIFBFUlRBSU5JTkcgVE8gVEhFIERJU1RSSUJVVElPTiBPRiBU SEUgU09GVFdBUkUgV0lUSE9VVA0KLy8gU1BFQ0lGSUMsIFdSSVRURU4gUFJJT1IgUEVSTUlTU0lP TjsgKDQpIEFMTCBDT0RFIERFUklWRUQgRlJPTSBUSElTIFNPRlRXQVJFDQovLyBCRSBFWEVDVVRF RCBXSVRIIFRIRSBNT0xFQ1VMQVIgT1BFUkFUSU5HIEVOVklST05NRU5UIChNT0UpIExJQ0VOU0VE IEZST00NCi8vIENIRU1JQ0FMIENPTVBVVElORyBHUk9VUCBJTkMuDQovLw0KLy8gQ0hFTUlDQUwg Q09NUFVUSU5HIEdST1VQIElOQy4gRElTQ0xBSU1TIEFMTCBXQVJSQU5USUVTIFdJVEggUkVHQVJE IFRPIFRISVMNCi8vIFNPRlRXQVJFLCBJTkNMVURJTkcgQUxMIElNUExJRUQgV0FSUkFOVElFUyBP RiBNRVJDSEFOVEFCSUxJVFkgQU5EIEZJVE5FU1MsDQovLyBBTkQgSU4gTk8gRVZFTlQgU0hBTEwg Q0hFTUlDQUwgQ09NUFVUSU5HIEdST1VQIElOQy4gQkUgTElBQkxFIEZPUiBBTlkNCi8vIFNQRUNJ QUwsIElORElSRUNUIE9SIENPTlNFUVVFTlRJQUwgREFNQUdFUyBPUiBBTlkgREFNQUdFUyBXSEFU U09FVkVSDQovLyBSRVNVTFRJTkcgRlJPTSBMT1NTIE9GIFVTRSwgREFUQSBPUiBQUk9GSVRTLCBX SEVUSEVSIElOIEFOIEFDVElPTiBPRg0KLy8gQ09OVFJBQ1QsIE5FR0xJR0VOQ0UgT1IgT1RIRVIg VE9SVElPVVMgQUNUSU9OLCBBUklTSU5HIE9VVCBPRiBPUiBJTg0KLy8gQ09OTkVDVElPTiBXSVRI IFRIRSBVU0UgT1IgUEVSRk9STUFOQ0UgT0YgVEhJUyBTT0ZUV0FSRS4NCi8vDQovKg0KDQpEZXNj cmlwdGlvbjoNCkNhbHVsYXRlIHRoZSBSTVMgYmV0d2VlbiB0d28gY2hhaW5zLiAgVHlwaWNhbCB1 c2UgaXMgZm9yIGNvbXBhcmluZyB0d28NCmxpZ2FuZCBjaGFpbnMuDQoNClVzaW5nOg0KLSBTYXZl IHRoZSBmaWxlICdybXMuc3ZsJyBpbiB5b3VyIH4vc3ZsIGRpcmVjdG9yeQ0KLSBMb2FkIHRoZSBm aWxlIHJtcy5zdmwnIHVzaW5nIHRoZSBNT0UgQ29tbWFuZCBXaW5kb3c6DQogc3ZsPiBsb2FkICdy bXMuc3ZsJyANCi0gVG8gY2FsY3VsYXRlIHRoZSBSTVMgYmV0d2VlbiAyIGNoYWlucywgaW4gdGhl IE1PRSBDb21tYW5kcyB3aW5kb3cgdHlwZToNCiBzdmw+IHJtc1tdDQoNCiovDQoNCg0KI3NldCB0 aXRsZQknUk1TIERpZmZlcmVuY2UnDQojc2V0IG1haW4JJ01PRV9STVMnDQoNCmdsb2JhbCBmdW5j dGlvbiBybXMgW10NCiAgICBsb2NhbCBhdG9tX2tleXMsIG51bV9hdG9tcywgY2hhaW5zOw0KICAg IGxvY2FsIG51bV9hdG9tczEsIG51bV9hdG9tczI7DQogICAgbG9jYWwgbGlnMSwgbGlnMV9haywg aGxpZzFfYWssIHBvczE7DQogICAgbG9jYWwgbGlnMiwgbGlnMl9haywgaGxpZzJfYWssIHBvczI7 DQogICAgbG9jYWwgcm1zOw0KDQogICAgYXRvbV9rZXlzID0gQXRvbXNbXTsNCiAgICBudW1fYXRv bXMgPSBuQXRvbXNbXTsNCiAgICBjaGFpbnMgPSBDaGFpbnNbXTsNCg0KICAgIGxpZzEgPSBjaGFp bnMoMSk7DQogICAgbGlnMiA9IGNoYWlucygyKTsNCg0KICAgIGxpZzFfYWsgPSBjYXQgY0F0b21z IGxpZzE7DQogICAgbGlnMl9hayA9IGNhdCBjQXRvbXMgbGlnMjsNCg0KICAgIGhsaWcxX2FrID0g bGlnMV9hayB8IGFBdG9taWNOdW1iZXIgbGlnMV9hayA+IDE7DQogICAgaGxpZzJfYWsgPSBsaWcy X2FrIHwgYUF0b21pY051bWJlciBsaWcyX2FrID4gMTsNCg0KICAgIG51bV9hdG9tczEgPSBsZW5n dGggaGxpZzFfYWs7DQogICAgbnVtX2F0b21zMiA9IGxlbmd0aCBobGlnMl9hazsNCg0KICAgIHdy aXRlWycgVG90YWwgbnVtYmVyIG9mIGF0b21zIGluIGVhY2ggbGlnYW5kID0ge31cbicsIChudW1f YXRvbXMvMikgXTsNCiAgICB3cml0ZVsnIE51bWJlciBvZiBoZWF2eSBhdG9tcyBpbiBlYWNoIGxp Z2FuZCA9IHt9XG4nLCBudW1fYXRvbXMxIF07DQoNCiAgICBwb3MxID0gYVBvcyBobGlnMV9hazsN CiAgICBwb3MyID0gYVBvcyBobGlnMl9hazsNCg0KLy8gICAgd3JpdGVbJ1Bvc2l0aW9ucyBvZiBB dG9tcyA9IHt9XG4nLHBvczFdOw0KLy8gICAgd3JpdGVbJ1Bvc2l0aW9ucyBvZiBBdG9tcyA9IHt9 XG4nLHBvczJdOw0KDQogICAgcm1zID0gc3FydCAoKGFkZCAoc3FyIChwb3MxKDEpIC0gcG9zMigx KSkgKyBzcXIocG9zMSgyKSAtIHBvczIoMikpDQogICAgICAgICAgICAgICAgKyBzcXIocG9zMSgz KSAtIHBvczIoMykpKSkgLyBudW1fYXRvbXMxKSA7DQoNCiAgICB3cml0ZVsnUk1TZCA9IHt9XG4n LHJtc107DQoNCmVuZGZ1bmN0aW9uDQo= ------_=_NextPart_002_01C74960.93E07F80-- ------_=_NextPart_001_01C790AE.F79B4B03-- From owner-chemistry@ccl.net Mon May 7 11:03:01 2007 From: "Phil Hultin hultin%a%cc.umanitoba.ca" To: CCL Subject: CCL: Interplane Angle Message-Id: <-34204-070507100542-17668-1alL6QYujQ7Wtfhj2E0L/Q.:.server.ccl.net> X-Original-From: "Phil Hultin" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Mon, 7 May 2007 09:05:02 -0500 MIME-Version: 1.0 Sent to CCL by: "Phil Hultin" [hultin(~)cc.umanitoba.ca] Basic geometry is one of the things many of us have forgotten (I include myself in this) but whenever I need such things I just google. It's humbling to be reminded that back in freshman year we all knew how to find things like the angle between two planes! If you google the phrase "angle between two planes" you will find thousands of web pages that give you the math - and then a few minutes work with your spreadsheet and you have your answer. Dr. Philip G. Hultin Professor of Chemistry, University of Manitoba Winnipeg, MB R3T 2N2 hultin===cc.umanitoba.ca http://umanitoba.ca/chemistry/people/hultin -----Original Message----- > From: owner-chemistry===ccl.net [mailto:owner-chemistry===ccl.net] Sent: May 6, 2007 11:07 PM To: Hultin, Philip G. Subject: CCL: Interplane Angle Sent to CCL by: "Sue L" [chsue2004|-|yahoo.com] Hi, Does anyone know a program that can measure an interplane angle from calculated structures? Many thanks Suehttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon May 7 11:38:00 2007 From: "Atul Agarwal aagarwal##achillion.com" To: CCL Subject: CCL: Looking for ways of RMSD calculation on different docking softwares Message-Id: <-34205-070507113713-10149-GrLzU+N0/v4gWg7BmapThQ- -server.ccl.net> X-Original-From: "Atul Agarwal" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Mon, 7 May 2007 11:36:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Atul Agarwal" [aagarwal(_)achillion.com] Sobia: Looks like the attachment did not go through. Here it is: #svl // rms.svl calculates the RMS between two chains (and only two) // // 01-feb-2003 (exe) Created // // COPYRIGHT (C) 1998-2007 CHEMICAL COMPUTING GROUP INC. ALL RIGHTS RESERVED. // // PERMISSION TO USE, COPY, MODIFY AND DISTRIBUTE THIS SOFTWARE IS HEREBY // GRANTED PROVIDED THAT: (1) UNMODIFIED OR FUNCTIONALLY EQUIVALENT CODE // DERIVED FROM THIS SOFTWARE MUST CONTAIN THIS NOTICE; (2) ALL CODE DERIVED // FROM THIS SOFTWARE MUST ACKNOWLEDGE THE AUTHOR(S) AND INSTITUTION(S); (3) // THE NAMES OF THE AUTHOR(S) AND INSTITUTION(S) NOT BE USED IN ADVERTISING // OR PUBLICITY PERTAINING TO THE DISTRIBUTION OF THE SOFTWARE WITHOUT // SPECIFIC, WRITTEN PRIOR PERMISSION; (4) ALL CODE DERIVED FROM THIS SOFTWARE // BE EXECUTED WITH THE MOLECULAR OPERATING ENVIRONMENT (MOE) LICENSED > FROM // CHEMICAL COMPUTING GROUP INC. // // CHEMICAL COMPUTING GROUP INC. DISCLAIMS ALL WARRANTIES WITH REGARD TO THIS // SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, // AND IN NO EVENT SHALL CHEMICAL COMPUTING GROUP INC. BE LIABLE FOR ANY // SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER // RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF // CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN // CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. // /* Description: Calulate the RMS between two chains. Typical use is for comparing two ligand chains. Using: - Save the file 'rms.svl' in your ~/svl directory - Load the file rms.svl' using the MOE Command Window: svl> load 'rms.svl' - To calculate the RMS between 2 chains, in the MOE Commands window type: svl> rms[] */ #set title 'RMS Difference' #set main 'MOE_RMS' global function rms [] local atom_keys, num_atoms, chains; local num_atoms1, num_atoms2; local lig1, lig1_ak, hlig1_ak, pos1; local lig2, lig2_ak, hlig2_ak, pos2; local rms; atom_keys = Atoms[]; num_atoms = nAtoms[]; chains = Chains[]; lig1 = chains(1); lig2 = chains(2); lig1_ak = cat cAtoms lig1; lig2_ak = cat cAtoms lig2; hlig1_ak = lig1_ak | aAtomicNumber lig1_ak > 1; hlig2_ak = lig2_ak | aAtomicNumber lig2_ak > 1; num_atoms1 = length hlig1_ak; num_atoms2 = length hlig2_ak; write[' Total number of atoms in each ligand = {}\n', (num_atoms/2) ]; write[' Number of heavy atoms in each ligand = {}\n', num_atoms1 ]; pos1 = aPos hlig1_ak; pos2 = aPos hlig2_ak; // write['Positions of Atoms = {}\n',pos1]; // write['Positions of Atoms = {}\n',pos2]; rms = sqrt ((add (sqr (pos1(1) - pos2(1)) + sqr(pos1(2) - pos2(2)) + sqr(pos1(3) - pos2(3)))) / num_atoms1) ; write['RMSd = {}\n',rms]; endfunction *Using rms.svl* - Save the file 'rms.svl' in your ~/svl directory - Load the file 'rms.svl' using the MOE Command Window: svl> load 'rms.svl' - To calculate the RMS between 2 ligands, in the MOE Commands window type: svl> rms[] - The results will be returned to the SVL Command Window Atul -----Original Message----- > From: owner-chemistry[*]ccl.net [mailto:owner-chemistry[*]ccl.net] Sent: Monday, May 07, 2007 4:06 AM To: Atul Agarwal Subject: CCL: Looking for ways of RMSD calculation on different docking softwares Sent to CCL by: "Sobia Ahsan Halim" [sobia_halim###yahoo.com] Dear All Hi. I am trying to redock compounds on the protein's active site.But I am facing so many problems. (1)I am working on MOE2006.08 and wants to calculate RMSD between the docked conformation of the ligand and the ligand in the complex structure of protein but I couldn't find any option to calculate RMSD. If anyone can tell me the best possible way to calculate RMSD on MOE2006.08 or SVL and can give me command to calculate RMSD on SVL, I will be deeply grateful. (2)I am also working on AutoDock Tools, I find least energy but very high RMSD or vice versa. What is the possible way to overcome this problem?. (3)Is there any posssibility to directly calculate RMSD between two ligands which are of different vectors on VMD?????.... (4)Is there any option to calculate RMSD on FlexiDock???... It will be highly appreciated if anyone can help me out.. Thanks in a million.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Mon May 7 12:21:00 2007 From: "Sarah Sparling sbs]_[ualberta.ca" To: CCL Subject: CCL: gar2ped Message-Id: <-34206-070507114434-15351-8iWIn9GjK2VVoOwz1gmQxQ.@.server.ccl.net> X-Original-From: "Sarah Sparling" Date: Mon, 7 May 2007 11:44:30 -0400 Sent to CCL by: "Sarah Sparling" [sbs]~[ualberta.ca] Hi, I'm trying to use gar2ped to calculate the frequencies of an isotope. I'm not quite sure how to interpret the output file. Does anyone know how, or know where I could get a free manual? sarah, sbs]-[ualberta.ca From owner-chemistry@ccl.net Mon May 7 15:37:00 2007 From: "Michel Petitjean ptitjean~~itodys.jussieu.fr" To: CCL Subject: CCL:G: Geometry symmetrizer code or algorithm? Message-Id: <-34207-070507153451-18760-kE6HsFgQB4BnX5brtgHYUA!^!server.ccl.net> X-Original-From: Michel Petitjean Date: Mon, 7 May 2007 21:34:40 +0200 (MEST) Sent to CCL by: Michel Petitjean [ptitjean ~~ itodys.jussieu.fr] To: chemistry]|[ccl.net Subject: CCL:Re:G: Geometry symmetrizer code or algorithm? It is an interesting question and a difficult problem. In the worst case, you have to consider highly dissymmetric sets. I am not aware of a fully general procedure symmetrizing a non symmetric set into a symmetric set, despite that some authors have attempted to do that. In the case of transforming a chiral set into an achiral one, some conditions to do that have been derived by me (Compt. Rend. Chim., 2006, 9[10],1249-1251, in french, english abstract; DOI 10.1016/j.crci.2006.03.003) It is related to chirality and symmetry measures (see my open access paper in Entropy 2003, 5[3], 271-312 http://www.mdpi.net/entropy/papers/e5030271.pdf Michel Petitjean, Email: petitjean]|[itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean]|[ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.html Sent to CCL by: "Kalju Kahn" [kalju-x-chem.ucsb.edu] > Hello, > > I am looking for a free program, algorithm examples, or pertinent literature > for symmetrizing almost symmetric molecular structures in Cartesian coordinates. > I am aware that several big programs (e.g. Gaussian, Maestro) have some built-in > capabilities to symmetrize structures but I am looking for a freely available code. > > Thank you, > > Kalju From owner-chemistry@ccl.net Mon May 7 22:01:01 2007 From: "Andrey.Bliznyuk ~ anu.edu.au" To: CCL Subject: CCL: Geometry symmetrizer code or algorithm? Message-Id: <-34208-070507192846-27268-CFZb8NSgysV8KSsEUi7gNw.:.server.ccl.net> X-Original-From: Andrey.Bliznyuk]|[anu.edu.au Date: Tue, 08 May 2007 08:53:38 +1000 Sent to CCL by: Andrey.Bliznyuk^^anu.edu.au Hi, Many years ago I looked at the problem in conjuction with Turbomole input generation, and it resulted in a program that's still available at http://sf.anu.edu.au/~aab900/ (click on "Symmetrization of Input Coordinates and Determination of Independent Variables") Another attemt I know about can be found at: http://www.cobalt.chem.ucalgary.ca/ps/ The idea behind the algorithm is simple: first you use some tolerance factor to determing what the symmetry is, then the generators of the point group found are used to generate an "improved" set of coordinates. Naturally, it only works for geometry that its not too far from symmetrical. Hope it helps. Dr Andrey Bliznyuk ANU Supercomputer Facility Leonard Huxley Bld.(#56) Canberra, ACT 0200 Australia