From owner-chemistry@ccl.net Mon Jun 12 03:22:00 2006 From: "Rajan Vatassery r-vatassery]_[northwestern.edu" To: CCL Subject: CCL: TINKER bad interpolation Message-Id: <-31924-060612021440-32006-AACo/mpdprKz8QgjfYIiOA..server.ccl.net> X-Original-From: "Rajan Vatassery" Date: Mon, 12 Jun 2006 02:14:39 -0400 Sent to CCL by: "Rajan Vatassery" [r-vatassery[-]northwestern.edu] Dear CCLers, I'm having a bit of a problem during a TINKER minimization. Many times a minimization I'm running will proceed through a few iterations (sometimes even a few hundred) and then crash out with the error LBFGS -- Incomplete Convergence due to BadIntpln. After going through a bit of the code, I noticed that this error is associated with the search.f subroutine, which performs a unidimensional line search. I also noticed that the last time I got this error (and possibly many other times as well), the angle between the search line and the negative gradient vector is almost 90 degrees. How can I avoid this error? It is happening in almost every run I do now. I believe that part of the cause of this problem is that I am calculating a system where I have no real atoms -- I have defined the types of all my atoms in the keyfile (included below). Thanks in advance, Rajan Vatassery Graduate Student r-vatassery a northwestern <> edu KEYFILE BEGINS BELOW: Force Field Selection PARAMETERS /home/rvatassery/tinkerinstall/params/mm3.prm ATOM 170 Bg "bulkygrp" 10 20.179 1 ATOM 171 Cm "chainatm" 10 20.179 3 CUTOFF 15.0 STEPMAX 0.2 ANGANGTERM NONE IMPROPTERM NONE IMPTORSTERM NONE OPBENDTERM NONE OPDISTTERM NONE STRBNDTERM NONE STRTORTERM NONE TORTORTERM NONE UREYTERM NONE VDW 170 15.000 0.100 VDW 171 0.005 0.000 BOND 170 171 1.0000 8.0000 BOND 171 171 2.5000 8.0000 ANGLE 171 171 171 0.670 180.000 ANGLE 171 171 170 1.000 90.000 TORSION 170 171 171 171 0.000 0.0 1 TORSION 170 171 171 170 0.000 0.0 1 TORSION 171 171 171 171 0.000 0.0 1 RESTRAIN-TORSION 31 1 2 32 5.0 0.0 0.0 RESTRAIN-TORSION 32 2 3 33 5.0 0.0 0.0 RESTRAIN-TORSION 33 3 4 34 5.0 0.0 0.0 RESTRAIN-TORSION 34 4 5 35 5.0 0.0 0.0 RESTRAIN-TORSION 35 5 6 36 5.0 0.0 0.0 RESTRAIN-TORSION 36 6 7 37 5.0 0.0 0.0 RESTRAIN-TORSION 37 7 8 38 5.0 0.0 0.0 RESTRAIN-TORSION 38 8 9 39 5.0 0.0 0.0 RESTRAIN-TORSION 39 9 10 40 5.0 0.0 0.0 RESTRAIN-TORSION 40 10 11 41 5.0 0.0 0.0 RESTRAIN-TORSION 41 11 12 42 5.0 0.0 0.0 RESTRAIN-TORSION 42 12 13 43 5.0 0.0 0.0 RESTRAIN-TORSION 43 13 14 44 5.0 0.0 0.0 RESTRAIN-TORSION 44 14 15 45 5.0 0.0 0.0 RESTRAIN-TORSION 45 15 16 46 5.0 0.0 0.0 RESTRAIN-TORSION 46 16 17 47 5.0 0.0 0.0 RESTRAIN-TORSION 47 17 18 48 5.0 0.0 0.0 RESTRAIN-TORSION 48 18 19 49 5.0 0.0 0.0 RESTRAIN-TORSION 49 19 20 50 5.0 0.0 0.0 RESTRAIN-TORSION 50 20 21 51 5.0 0.0 0.0 RESTRAIN-TORSION 51 21 22 52 5.0 0.0 0.0 RESTRAIN-TORSION 52 22 23 53 5.0 0.0 0.0 RESTRAIN-TORSION 53 23 24 54 5.0 0.0 0.0 RESTRAIN-TORSION 54 24 25 55 5.0 0.0 0.0 RESTRAIN-TORSION 55 25 26 56 5.0 0.0 0.0 RESTRAIN-TORSION 56 26 27 57 5.0 0.0 0.0 RESTRAIN-TORSION 57 27 28 58 5.0 0.0 0.0 RESTRAIN-TORSION 58 28 29 59 5.0 0.0 0.0 RESTRAIN-TORSION 59 29 30 60 5.0 0.0 0.0 RESTRAIN-TORSION 60 30 31 61 5.0 0.0 0.0 ANGLEUNIT (scales E) From owner-chemistry@ccl.net Mon Jun 12 04:57:00 2006 From: "Joachim Sauer stc2006],[chemie.hu-berlin.de" To: CCL Subject: CCL: STC2006: Reminder Message-Id: <-31925-060612045352-7655-UI6tqm9BNCzcdESD3ZqyzQ]|[server.ccl.net> X-Original-From: "Joachim Sauer" Date: Mon, 12 Jun 2006 04:53:47 -0400 Sent to CCL by: "Joachim Sauer" [stc2006]=[chemie.hu-berlin.de] Dear colleague, the registration for the 42nd Symposium on Theoretical Chemistry "Quantum Chemistry - Methods and Applications" on September 3-6, 2006 in Erkner (near Berlin) closes soon. Please not that an increased fee applies and that we cannot guarantee accommodation at the conference site if you register after June, 16th. June 16 is also the deadline for submission of abstracts for oral presentations. Details can be found on the Internet: http://www.chemie.hu-berlin.de/ag_sauer/stc2006/index.html Looking forward to your application, Joachim Sauer (Chairman) From owner-chemistry@ccl.net Mon Jun 12 05:31:02 2006 From: "Yama Yama yamafuji6[-]yahoo.com" To: CCL Subject: CCL:G: Transition dipole in g03 Message-Id: <-31926-060612051744-22835-EQwFv3o0Kmc6bEgkcRRNCg/./server.ccl.net> X-Original-From: "Yama Yama" Date: Mon, 12 Jun 2006 05:17:42 -0400 Sent to CCL by: "Yama Yama" [yamafuji6]=[yahoo.com] Can any one tell me how to calculate the transition dipole when I do TDDFT calculation using g03? and how to assign the charge transfer character from such calculations? From owner-chemistry@ccl.net Mon Jun 12 06:53:01 2006 From: "Qing Shao shaoqingfly1981(-)gmail.com" To: CCL Subject: CCL: About the GCMD Message-Id: <-31927-060612065119-29051-H2tDo0J4uG/vD7Wq03cdew%%server.ccl.net> X-Original-From: "Qing Shao" Date: Mon, 12 Jun 2006 06:51:17 -0400 Sent to CCL by: "Qing Shao" [shaoqingfly1981() gmail.com] cclers: Hi, cclers. I am looking for the code of GCMD(Dual Volume Control Grand Canonical Molecular Dynamics). Could you tell me if there is any codes I can gain under the GPL? From owner-chemistry@ccl.net Mon Jun 12 07:28:01 2006 From: "Ulrike Salzner salzner-#-fen.bilkent.edu.tr" To: CCL Subject: CCL: relative signs of orbitals Message-Id: <-31928-060612064013-27878-DFeECIbjLmOglzDr6tBeVQ:-:server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Mon, 12 Jun 2006 13:40:02 +0300 Mime-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner|fen.bilkent.edu.tr] Many thanks to Huub, Igor, Georg, Daniel, and Noel for your comments on signs of orbitals in open-shell TDDFT calculations, explaining that the signs of the MO coefficients are indeed arbitrary. Therefore the relative signs of excitations of alpha and beta electrons in the CI expansion are arbitrary as well. Since the messages were posted to CCl, I did not repost a summary. Ulrike -- Ulrike Salzner Associate Professor Department of Chemistry Bilkent University 06800 Bilkent, Ankara Turkey From owner-chemistry@ccl.net Mon Jun 12 08:03:00 2006 From: "Judith Bandy jbandy/a\inforsense.com" To: CCL Subject: CCL: Free Live Webcasts Message-Id: <-31929-060612073059-17534-gK1ftkuwBwW0CU+N/IJaxg||server.ccl.net> X-Original-From: "Judith Bandy" Date: Mon, 12 Jun 2006 07:30:55 -0400 Sent to CCL by: "Judith Bandy" [jbandy]_[inforsense.com] You are invited to join two free webcasts..... _______________________________________________________________________ EVENT: How Workflows Help Biotechs......Reduce the cost of high quality, high volume data analysis by using InforSense KDE Date and Time: Wednesday, 14 June 2006 3:00pm UK /10:00am EST/7:00am PST 6:00pm UK /1:00pm EST/10:00am PST Presenters: Anthony Arvanites, Cheminformatics, Cambria BioSciences Robin Munro, Director Strategic Application Development, InforSense Duration: 45 minutes Cambria BioSciences is an innovative biotechnology company that combines the power of genetics, physiological disease models and high-throughput chemical screening to discover new drug leads and how they work. The company has a focused research agenda requiring intensive analytical work but has limited IT resources. In 2005, Cambria acquired InforSense KDE as the main tool for implementing their data analysis tasks. In this webcast, Tony Arvanites from Cambria BioSciences will describe how they rapidly implemented a custom portal of analytic applications, including compound inventory, high content screening analysis and predictive ADME, without needing to expand its IT resources. Cambria report savings in IT resources of around 35% through providing scientists with deployed applications built using InforSense KDE. Further details and registration to join the live webcast: http://www.inforsense.com/webcast_jun06_14.html _____________________________________________________ EVENT: Accessible Text Mining for Bioinformaticians - Using InforSense KDE to create and execute integrative bio- and text-analytic workflows Date and Time: Wednesday, 28 June 2006 3:00pm UK / 10:00am EST / 7:00am PST 6:00pm UK / 1:00pm EST / 10:00am PST Presenters: Alex Michie, Manager Application Development, InforSense Judith Bandy, Director Marketing Communications, InforSense Duration: 45 minutes The value of combining text analysis with bio-, chem- and clinical informatics methods is widely recognized for optimizing R&D decision-making. However, such highly relevant text information is not always readily accessible to researchers and can be difficult and time-consuming to access, process and analyze. This webcast will demonstrate how InforSense KDE enables bioinformaticians to combine bioinformatics and text analytics by using a workflow-based integrative analytics methodology that defines and streamlines research processes. It will include a tutorial on the basic principles of text analytics to exploit free-text resources for R&D decision-making. Further details and registration to join the live webcast: http://www.inforsense.com/webcast_jun06_28.html _________________________________________________________ Regards, Judith Bandy InforSense Ltd 459a Fulham Road Chelsea, London SW10 9UZ - UK InforSense - USA 25 Moulton Street, Cambridge, MA 02138 - USA www.inforsense.com (c) 2006 InforSense Ltd. All rights reserved. InforSense, the InforSense logo and TextSense are registered trade-marks of InforSense Ltd. Open Discovery Workflow is a trademark of InforSense Ltd. All other brands or products names are trademarks of their respective holders. From owner-chemistry@ccl.net Mon Jun 12 08:38:00 2006 From: "Anand Krishnamurthy anand{=}loyolacollege.edu" To: CCL Subject: CCL: Reg: 2D to 3D conversion Message-Id: <-31930-060612062818-26523-WiJ0k7+XLdBv8jh9ufx3yg]~[server.ccl.net> X-Original-From: "Anand Krishnamurthy" Date: Mon, 12 Jun 2006 06:28:17 -0400 Sent to CCL by: "Anand Krishnamurthy" [anand ~~ loyolacollege.edu] Greeeting to one and all, I have really been benefitted extensively from an update to mechanise many problems on computational chemistry. I would like to know the algorithm involved in converting a two dimensional molecular structure data file into a three dimensional one.Another question is that how do I calculate manually gasteiger charges for small molecules and further can I automate to place charges on all of the similar atoms in molecules. Thanks and regards Anand From owner-chemistry@ccl.net Mon Jun 12 09:13:02 2006 From: "Tom Sundius Tom.Sundius..helsinki.fi" To: CCL Subject: CCL: B Matrix in GAMESS-US - Bug? Message-Id: <-31931-060612052715-26151-PwOWsSngoSI1tSVnbGuVig(0)server.ccl.net> X-Original-From: Tom Sundius Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 12 Jun 2006 11:45:06 +0300 (EEST) MIME-Version: 1.0 Sent to CCL by: Tom Sundius [Tom.Sundius^helsinki.fi] Gustavo Mercier asked about a problem he thinks he has found with the torsion routine TORS in the GAMESS module zmatrx.src. As far as I can see it is identical to the routine with the same name in Schachtschneider's program GMAT (see Vibrational Analysis of Polyatomic Molecules V, Techn. Report No. 231-64, Shell Development Company, Emeryville, California 1964). In the GAMESS module it is mentioned that a (wellknown?) sign error in the second term of equation 22 on p. 61 of Wilson, Decius, Cross: Molecular Vibrations (1955) has been corrected. This sign error has been mentioned in several papers, for instance in W.F. Murphy, Can. J. Chem. 69 (1991) 1672, and was corrected in the Dover republication (1980). However, the sign error is still present in equation (4.4.29) of S. Califano: Vibrational States (Wiley, 1976). Concerning the scalar product, Gustavo Mercier correctly states that cos (angle_1) should be calculated as e21 (dot) e23, where the unit vectors are directed towards the bond end atoms. However, checking the code in the TORS routine (lines 1853-1858 in my copy), it seems that the scalar product is computed as -e12 (dot) e23, which should give the correct result (the other scalar product that was mentioned is computed as -e23 (dot) e34, which is similar). If there is a problem, I suppose it is somewhere else in the code. By the way, in the above mentioned paper by W.F. Murphy there is a simple example which could be used to check the B-matrix calculation. Best regards, Tom Sundius On Wed, 7 Jun 2006, Gustavo A Mercier gamercier[a]yahoo.com wrote: > Sent to CCL by: "Gustavo A Mercier" [gamercier(-)yahoo.com] > Hi! > > I might have found a bug in GAMESS-US... but before I make any claims I > would like a second opinion. > I am encoding the B matrix the converts infinitesimal cartesian > displacements to internal coordinate displacements. This matrix is used > in the theory of molecular vibrations and the generation of delocalized > coordinates, etc. > > To check my code I've compared the output from GAMESS-US subroutines in > zmatrx.src. However, there are differences in the B matrices I compute > and the one computed with the GAMESS-US code.These are associated with > the torsion angle terms. After looking at the code in GAMESS-US and the > formulae in Molecular Vibrations by Wilson, Decius, and Cross, pub. Dover > 1980, I find the following discrepancy: > > In computing the matrix elements for the torsion angles 1,2,3,4, ie. the > angle between the planes 123 and 234 with the atoms 1 and 4 at the ends, > and 2 and 3 along the line of sight with 2 closest to the viewer > > 1 1 > \ bend | > \ angle 1 | > \ | torsion angle > 2 -------- 3 23 > \ \ > bend angle 2 \ \ > \ 4 > 4 > > i = 1, j = 2, k = 3, l = 4 > >> From Wilson's book: > > Cos(angle_1) = Dot(2--1>,2-->3) where i-->j is a unit vector from i to j > Cos(angle_2) = Dot(3-->2,3-->4) and Dot is the cartesian dot product > > However in GAMESS-US the code (subroutine BTORS in zmatrx.src) computes > > Cos(angle_1) = Dot(1-->2,2-->3) > Cos(angle_2) = Dot(2-->3,3-->4) > > There is a reversal in the orientation of the first unit vector associated > with the first bond that makes the angle. > > The end result is that there is a sign reversal in the Cos terms between > the two programs. I don't see this "corrected" in the remainder of the code. > > Anyone who can shed any light on this discrepancy, beyond stating that > there is a bug in the GAMESS-US code or a typographical error in the 1980 > edition of Wilson's book? (I am familiar with Wilson's definition, so I > favor an error in GAMESS-US. However, before I make any claims I would > appreciate > a second opinion!) > > Neither one of the codes generates B matrices that reproduce the delocalized > coordinates for the fluoroethylene example in Baker's et al J. Chem. Phys. > 105(1) 192-212 (1996). > > Thanks! > Gustavo Mercier > From owner-chemistry@ccl.net Mon Jun 12 10:18:00 2006 From: "Shobe, David dshobe{:}sud-chemieinc.com" To: CCL Subject: CCL: parameters Message-Id: <-31932-060612101505-23282-+TjqmewJBQNzeb9ynCiOgQ ~~ server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 12 Jun 2006 16:14:12 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe===sud-chemieinc.com] I take it you want the N and O atoms to just bounce off each other, as if they were inert gases, without a chance to form molecules? You might be able to do this as follows. Calculate the surface of N+N, but with the nitrogen atoms having parallel spins, so that they cannot form N2. Since each N atom is a quartet (3 spins), the N+N system would then be a septet (6 spins). Similarly calculate N+O as a sextet (3+2=5 spins) and O+O as a quintet (2+2=4 spins). You can use this potential to construct the MD parameters. Anything you do is going to be somewhat arbitrary, since you're asking the atoms to behave in ways contrary to their nature (which is to combine). BTW: How are you handling the force between the N and O atoms and the SiO2 surface? --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry-#-ccl.net [mailto:owner-chemistry-#-ccl.net] Sent: Saturday, June 10, 2006 12:11 PM To: Shobe, David Subject: CCL: parameters Sent to CCL by: Ioana Cozmuta [ioana .. nas.nasa.gov] Hi CCL users, I am not sure if this is the best place to ask but I couldn't think of a better one. I want to do MD simulations of a gas formed by a mix of ATOMIC nitrogen and oxygen (N, O) interacting with a SiO2 surface at high temperatures (>800K). What would be the best empirical parameters (on- and off-diagonal) van der Waals interactions of N and O (again atoms and not molecules) to use? For the SiO2 surface I am using Morse stretch parameters from the MSQ force field by Demiralp et al. So far I tried the Dreiding parameters for O and N but I was wondering if anyone has done or knows of any refinement. Thank you, Ioana -- Ioana Cozmuta, Ph.D Eloret Corporation NASA Ames Research Center Mail Stop 230-3 Moffett Field, CA 94035 phone (650) 604-0993 e-mail: icozmuta^-^mail.arc.nasa.gov http://people.nas.nasa.gov/~ioana/http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you.