From owner-chemistry@ccl.net Wed Aug 22 03:04:00 2007 From: "Egon Willighagen egon.willighagen * gmail.com" To: CCL Subject: CCL: Open Source 3D coordinate generation tool Message-Id: <-34974-070822025447-24068-Hgdlu5HBfHy3gjjzmxJz7g]^[server.ccl.net> X-Original-From: "Egon Willighagen" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 22 Aug 2007 08:54:10 +0200 MIME-Version: 1.0 Sent to CCL by: "Egon Willighagen" [egon.willighagen[*]gmail.com] Hi Rajarshi, On 8/21/07, Rajarshi Guha rguha:-:indiana.edu wrote: > Sent to CCL by: Rajarshi Guha [rguha]_[indiana.edu] > > - Is there any specific reason for Apache license? Do you think it > > might present difficulties for people who'd like to include this project in > > their GPL code? > > My understanding is that the Apache license is very permissive and > that the code can be included in GPL and related code. At least with GPL2 this is not possible. GPL3 was planned to be compatible, but have not read that yet. Egon -- ---- http://chem-bla-ics.blogspot.com/ From owner-chemistry@ccl.net Wed Aug 22 04:03:00 2007 From: "Oellien, F (Frank) Frank.Oellien=-=Intervet.com" To: CCL Subject: CCL: Open Source 3D coordinate generation tool Message-Id: <-34975-070822040058-23910-frxas/4RFX6MuFTYTaVqVA=-=server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 22 Aug 2007 10:00:34 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [Frank.Oellien/./Intervet.com] Hello, Nice work. I will compare your tool with Corina. I think it is important that the smi2sdf tool should accept sdf as input. As I understand the tool is not only transforming a SMILES string to a SD file. Rather smi2sdf is also responsible to generate a rough §d structure that will be optimized with mengine. I think that using mengine on SD files containi9ng 2D coordinates will take much longer compared to SD files containing rough 3D coordinates. Mit freundlichen Grüßen / With kind regards Dr. Frank Oellien Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien|,|intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com Intervet Innovation GmbH is an Akzo Nobel company Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschäftsführer: Dr. Peter Schmid > > On 8/20/07, Rajarshi Guha rguha^^indiana.edu > wrote: > > Sent to CCL by: Rajarshi Guha [rguha===indiana.edu] The program and > > instructions of compiling and usage can be obtained from > > http://www.chembiogrid.org/cheminfo/smi23d/ > -------------------------------------- This message, including attachments, is confidential and may be privileged. If you are not an intended recipient, please notify the sender then delete and destroy the original message and all copies. You should not copy, forward and/or disclose this message, in whole or in part, without permission of the sender. -------------------------------------- From owner-chemistry@ccl.net Wed Aug 22 04:38:00 2007 From: "Heribert Reis hreis||eie.gr" To: CCL Subject: CCL: Fractional coordinates to cartesian Message-Id: <-34976-070821132517-6934-oVS5ofrK3YuyycctTn+j7A]=[server.ccl.net> X-Original-From: Heribert Reis Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 21 Aug 2007 18:24:58 +0300 MIME-Version: 1.0 Sent to CCL by: Heribert Reis [hreis * eie.gr] Hi, the cartesian coordinates x,y,z of fractional coordinates f,g,h in a crystal with unit cell lengths a,b,c and angles alp,bet,gam are given by a symmetric 3x3 trafo-matrix T with elements T11 = a T12 = b cos(gam) T13 = c cos(bet) T22= b sin(gam) T23=c [ cos(alp)-cos(bet) cos(gam) ] / sin(gam) T33=c/sin(gam) Sqrt [ 1-{cos^2(alp)+cos^2(bet)+cos^2(gam)} + 2cos(alp) cos(bet) cos(gam) ] so (x,y,z) = T . (f,g,h). I suppose these eqs are given somewhere in the International Tables of Crystallography (may be a good idea to check them). They simplify considerably in orthorhombic unit cells, then x= a f; y = b g; z=c h. Cheers, Heribert > Sent to CCL by: "Richard Leo Wood" [woodx278 ~~ umn.edu] > Hi all, > > Do any of you know of any program (free?) that will convert fractional coordinates to cartesian coordinates? If not in a program, is there a method that can be used to do it? I spent most of yesterday searching for something, but I came up empty. > > I have a few crystal structures in fractional coordinates (in papers, so I don't have them in electronic format) that I need converted to cartesian to compare them to some calculations that I have done. > > TIA, > Richard > > > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278[]umn.edu> > > > > From owner-chemistry@ccl.net Wed Aug 22 08:34:00 2007 From: "Aviva Litovitz ael23=cornell.edu" To: CCL Subject: CCL:G: ADMP initial velocities Message-Id: <-34977-070821215144-21725-HMXrxJ2fZMORFvJNPL+Uyw(a)server.ccl.net> X-Original-From: "Aviva Litovitz" Date: Tue, 21 Aug 2007 21:51:40 -0400 Sent to CCL by: "Aviva Litovitz" [ael23-$-cornell.edu] I am trying to run ADMP trajectories in gaussian by entering in initial velocities (ReadMWVelocity) but it only seems to work if these velocities are very small. With larger velocities (~10^13 amu1/2*Bohr/sec), after the initial position, the calculation stops or the energy balloons and the coordinates turn into asterisks. Any suggestions? Thanks, Aviva From owner-chemistry@ccl.net Wed Aug 22 09:08:00 2007 From: "H H abdallah hwchems=-=yahoo.com" To: CCL Subject: CCL: research Message-Id: <-34978-070822022410-19604-tMzFEfjrpd8pX5/cyyFrpg|a|server.ccl.net> X-Original-From: "H H abdallah" Date: Wed, 22 Aug 2007 02:24:07 -0400 Sent to CCL by: "H H abdallah" [hwchems(a)yahoo.com] Hello, I am researcher in the field of theoretical chemistry (QM, MM, MD simulation ...). Is there any scientist in any field who would like to do research in this field? I have all the important software for that research and I want to be the end of this work a publication. Regards From owner-chemistry@ccl.net Wed Aug 22 11:06:01 2007 From: "gord gayers07!^!cogeco.ca" To: CCL Subject: CCL: conversion to xyz Message-Id: <-34979-070821183213-31726-CIMcBhD/TB5iCA2379mA8Q.@.server.ccl.net> X-Original-From: "gord" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Tue, 21 Aug 2007 16:56:42 -0500 MIME-Version: 1.0 Sent to CCL by: "gord" [gayers07.:.cogeco.ca] I 'm not sure it's what you want but I have a small DOS program that will convert fractional coordinates to xyz format. I have both the executable and the source. I think it came from the CCL archive Gord ----- Original Message ----- > From: "Jon Lyon jtl3z]~[virginia.edu" To: "Ayers, Gordon W. " Sent: Tuesday, August 21, 2007 6:55 AM Subject: CCL: conversion to xyz > > Sent to CCL by: "Jon Lyon" [jtl3z*_*virginia.edu] > Does anyone know of a program (or have a script) to convert the atomic > distances of a molecule to an xyz file (or z-matrix)? > > Thanks if advance> > > > > > -- > No virus found in this incoming message. > Checked by AVG Free Edition. > Version: 7.5.484 / Virus Database: 269.12.1/963 - Release Date: 20/08/2007 > 5:44 PM > > From owner-chemistry@ccl.net Wed Aug 22 11:41:01 2007 From: "Pau Farr s pfarras^^icmab.es" To: CCL Subject: CCL: NBO CHOOSE keyword Message-Id: <-34980-070822092525-22647-hnR6G9kgjLoPyytDwVW8Og{=}server.ccl.net> X-Original-From: "Pau Farr s" Date: Wed, 22 Aug 2007 09:25:21 -0400 Sent to CCL by: "Pau Farr s" [pfarras~~icmab.es] Hello, I'm trying to send an NBO calculation from one of my compounds and there's no way it works. This is my input: NBO 3CBOND END CHOOSE lone 1 2 end bond s 1 2 s 1 3 s 1 23 s 1 24 end END And the error: NATURAL BOND ORBITAL ANALYSIS: Error in input of bond orbitals: Keyword for orbital type is not LONE, BOND, or 3CBOND (read `1 ') I don't want to specify all the lone pairs, bonds and 3cbonds because my molecule is rather big. I've tried to put only the 3cbond keyword and I get only 2 units (instead of 10 that I get without it) but I need only 1 unit, so I'm putting these bonds. Can someone help me please? Thanks! From owner-chemistry@ccl.net Wed Aug 22 12:25:02 2007 From: "Richard Leo Wood woodx278^^^umn.edu" To: CCL Subject: CCL: my question of yesterday: fractional coordinates to cartesian Message-Id: <-34981-070822115456-23808-oa2vGKIodCz/FWPdZTx7Xw]=[server.ccl.net> X-Original-From: "Richard Leo Wood" Date: Wed, 22 Aug 2007 11:54:53 -0400 Sent to CCL by: "Richard Leo Wood" [woodx278**umn.edu] Hi all, Yesterday, I posted a question about converting fractional coordinates to cartesian coordinates. A number of you responded and helped me at least to understand crystal structures a little bit better :) I learned that OpenBabel SHOULD do this, but it won't, at least not for me, not on any of the machines that I have access to (two pc's here and one at home). Even version 2.1.1 doesn't convert my .fract file to an xyz file. I would like to be able to do this myself (without having to rely on someone else to convert the .fract files I've created), but I'm at my wit's end. I've even tried a program called converte, but that doesn't work, either. I'd really appreciate a suggestion to a program that will work for me. TIA, Richard Richard L. Wood, Ph. D. University of Minnesota Dept. of Medicinal Chemistry, College of Pharmacy 717 Delaware St. SE Minneapolis, MN 55414-2959 woodx278**umn.edu From owner-chemistry@ccl.net Wed Aug 22 15:58:00 2007 From: "LI Daobing lidaobing+ccl{}gmail.com" To: CCL Subject: CCL: my question of yesterday: fractional coordinates to cartesian Message-Id: <-34982-070822152122-19390-6i8k+Lz3DnZp1ZWrL4Gp8Q!=!server.ccl.net> X-Original-From: "LI Daobing" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 23 Aug 2007 02:56:00 +0800 MIME-Version: 1.0 Sent to CCL by: "LI Daobing" [lidaobing+ccl*gmail.com] On 8/22/07, Richard Leo Wood woodx278^^^umn.edu wrote: > > Sent to CCL by: "Richard Leo Wood" [woodx278**umn.edu] > Hi all, > > Yesterday, I posted a question about converting fractional coordinates to cartesian coordinates. A number of you responded and helped me at least to understand crystal structures a little bit better :) > > I learned that OpenBabel SHOULD do this, but it won't, at least not for me, not on any of the machines that I have access to (two pc's here and one at home). Even version 2.1.1 doesn't convert my .fract file to an xyz file. > > I would like to be able to do this myself (without having to rely on someone else to convert the .fract files I've created), but I'm at my wit's end. I've even tried a program called converte, but that doesn't work, either. > > I'd really appreciate a suggestion to a program that will work for me. > have you tried mercury? http://www.ccdc.cam.ac.uk/free_services/mercury/ -- LI Daobing From owner-chemistry@ccl.net Wed Aug 22 18:05:01 2007 From: "Manali Joshi manali_+_adrik.bchs.uh.edu" To: CCL Subject: CCL: Looking for freeware to compute Tanimoto coefficient Message-Id: <-34983-070822180414-26918-yE/IonOS8NCeWaM0Q6MGiQ : server.ccl.net> X-Original-From: "Manali Joshi" Date: Wed, 22 Aug 2007 18:04:11 -0400 Sent to CCL by: "Manali Joshi" [manali- -adrik.bchs.uh.edu] Hello, I am looking for freeware to compute the Tanimoto coefficients between small molecules. Specifically i would like to compare a few molecules against a small database. Thanks in advance. -Manali From owner-chemistry@ccl.net Wed Aug 22 20:03:01 2007 From: "Terry Stephenson imslrecipes{:}yahoo.com" To: CCL Subject: CCL:G: O2 X Sigma_g triplet to B Sigma_u triplet transition Message-Id: <-34984-070822131657-12058-ESZT2ZcAMNC+6f6mVT3d/w .. server.ccl.net> X-Original-From: "Terry Stephenson" Date: Wed, 22 Aug 2007 13:16:53 -0400 Sent to CCL by: "Terry Stephenson" [imslrecipes]![yahoo.com] Hi Computational Chemists! I am totally new to Gaussian03 and would like to do some simple calculations for molecular oxygen. I would like to calculate two potential surfaces (actually curves since the internuclear distance is the only variable) of O2, i.e., the ground state X Sigma_g triplet and one of the excited states, i.e., B Sigma_g triplet, both states are "-" in parity. Moreover, I would like to calculate the transition dipole between the two states as a function of the internuclear distance. I read part of the Gaussian docs but thought some of you must have done this, so I thought to ask for your help. Thank you in advance! --Terry From owner-chemistry@ccl.net Wed Aug 22 20:52:01 2007 From: "Konstantin Kudin konstantin_kudin~!~yahoo.com" To: CCL Subject: CCL:G: ADMP initial velocities Message-Id: <-34985-070822200249-6075-HdX8MIWNneCoXK+O0thGxA%server.ccl.net> X-Original-From: Konstantin Kudin Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 22 Aug 2007 16:02:28 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Konstantin Kudin [konstantin_kudin.:.yahoo.com] Hi Aviva, Perhaps, the first thing to try is to check if the BOMD could run with the same input. If that is OK, then your problem could be due to the following. When the velocities are set to large values, the nuclei are suddenly moving fast, but the wavefunctions are still sitting dormant and have no velocities (at {t-dt} and {t} they were the same). So the nuclei might be running away from the electrons, before those had a chance to catch up. To fix this one could input velocities, do a few BOMD steps, and then restart with ADMP such that the wavefunctions at this point are moving in sync with the nuclei. Please post back if this helped. Regards, Konstantin --- "Aviva Litovitz ael23=cornell.edu" wrote: > > Sent to CCL by: "Aviva Litovitz" [ael23-$-cornell.edu] > I am trying to run ADMP trajectories in gaussian by entering in > initial velocities (ReadMWVelocity) but it only seems to work if > these velocities are very small. With larger velocities (~10^13 > amu1/2*Bohr/sec), after the initial position, the calculation stops > or the energy balloons and the coordinates turn into asterisks. Any > suggestions? > Thanks, > Aviva > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > > > ____________________________________________________________________________________ Be a better Heartthrob. Get better relationship answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545433 From owner-chemistry@ccl.net Wed Aug 22 22:38:01 2007 From: "Vincent Xianlong Wang xloongw]^[yahoo.com" To: CCL Subject: CCL: my question of yesterday: fractional coordinates to cartesian Message-Id: <-34986-070822213901-29020-4hPUVTgXOF6FXrfBj3gHyA]-[server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Wed, 22 Aug 2007 17:38:37 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw%a%yahoo.com] Hi Richard, I have Mathematica code for your purpose. If you have access to Mathematica 5.2, I can share the code with you. Best regards, Vincent --- "Richard Leo Wood woodx278^^^umn.edu" wrote: > > Sent to CCL by: "Richard Leo Wood" > [woodx278**umn.edu] > Hi all, > > Yesterday, I posted a question about converting > fractional coordinates to cartesian coordinates. A > number of you responded and helped me at least to > understand crystal structures a little bit better :) > > I learned that OpenBabel SHOULD do this, but it > won't, at least not for me, not on any of the > machines that I have access to (two pc's here and > one at home). Even version 2.1.1 doesn't convert my > .fract file to an xyz file. > > I would like to be able to do this myself (without > having to rely on someone else to convert the .fract > files I've created), but I'm at my wit's end. I've > even tried a program called converte, but that > doesn't work, either. > > I'd really appreciate a suggestion to a program that > will work for me. > > TIA, > Richard > > Richard L. Wood, Ph. D. > University of Minnesota > Dept. of Medicinal Chemistry, > College of Pharmacy > 717 Delaware St. SE > Minneapolis, MN 55414-2959 > woodx278]![umn.edu > > > > -= This is automatically added to each message by > the mailing script =- > To recover the email address of the author of the > message, please change > the strange characters on the top line to the \a/ > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST\a/ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > ____________________________________________________________________________________ Pinpoint customers who are looking for what you sell. http://searchmarketing.yahoo.com/