From owner-chemistry@ccl.net Thu Aug 25 03:43:04 2005 From: "CCL" To: CCL Subject: CCL: W:GAMESS input question Message-Id: <-28997-050824152536-8157-uNy46x+EILo1kNckC1/Z/g#%#server.ccl.net> X-Original-From: "Tony Yuan" Sent to CCL by: "Tony Yuan" [tyuan#%#camsoft.com] Can more than 1 ORIGIN(i), XVEC(i) and YVEC(i) be set in GRID group? If yes, how to set? A sample will be very appreciated. I tried following format: INPUT CARD> GRID INPUT CARD>ORIGIN(1)=0.0, 0.0, 1.0 INPUT CARD>XVEC(1)=2.0, 0.0, 1.0 INPUT CARD>YVEC(1)=0.0, 2.0, 1.0 INPUT CARD>ORIGIN(2)=0.0, 0.0, 1.1 INPUT CARD>XVEC(2)=2.0, 0.0, 1.1 INPUT CARD>YVEC(2)=0.0, 2.0, 1.1 INPUT CARD>SIZE=0.2 INPUT CARD>UNITS=ANGS INPUT CARD> END It doesnt work. Sincerely -Tony From owner-chemistry@ccl.net Thu Aug 25 07:51:32 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-28998-050825043131-18010-sJTYeKniThUXNerGpwThRw%a%server.ccl.net> X-Original-From: "Mgr. Lubos Vrbka" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: "Mgr. Lubos Vrbka" > Why not put a gold slab thru the middle, and use standard 3D PBC? You > get twice the surface area that way as well. in this case it would be probably better to use 3D PBC with slab correction to ewald summation provided by gromacs (type 3dbc). i think this will provide better results than 2D PBC that are very computationally inefficient (when compared to 3D) dlpoly package provides true "slab" PBC. i'm not sure how the long-range electrostatics is handled in this case, though. best regards, lubos -- ..................................................... Mgr. Lubos Vrbka Center for Biomolecules and Complex Molecular Systems Institute of Organic Chemistry and Biochemistry Academy of Sciences of the Czech Republic Prague, Czech Republic ..................................................... From owner-chemistry@ccl.net Thu Aug 25 09:20:01 2005 From: "CCL" To: CCL Subject: CCL: W:molecular orbitals for multiple k points ? Message-Id: <-28999-050825091847-17955-sJTYeKniThUXNerGpwThRw-,-server.ccl.net> X-Original-From: "peter martin ryan" Sent to CCL by: "peter martin ryan" Hi all I have been using Dmol 3 to examine reaction profiles for some organic molecules on the Silicon 100 surface in a peiodic regime. With Dmol you have the option of creating 3D plots of DFT molecular orbitals in the molecular case and periodic case. Computation of orbitals is possible for molecules and for periodics that use the Gamma-point, but not for periodic cases with multiple k-points. Is there any way to examine the molecular orbitals for periodics at K points other than the gamma point...specifically the HOMO and LUMO levels at other K points. Or does anyone know of some program that may facilate this analysis.. thanking you all in advance. Peter Ryan SFI Boland Lab Chemistry Dept. Trinity College Dublin. College Green Dublin 2 phone +353 (0)1 6083143 From owner-chemistry@ccl.net Thu Aug 25 10:35:19 2005 From: "CCL" To: CCL Subject: CCL: Software convert 3D structure .sd file to 2D structure Message-Id: <-29000-050825103252-5149-sJTYeKniThUXNerGpwThRw(a)server.ccl.net> X-Original-From: "Compchem List" content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5A981.DE269300" MIME-Version: 1.0 Sent to CCL by: "Compchem List" This is a multi-part message in MIME format. ------_=_NextPart_001_01C5A981.DE269300 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 Hi all, Could anybody suggest a software could convert 3D structure file (.sd or =2Emol) to a 2D structure file for synthetic chemists reading? Thanks in advance, William -------------------------------- William Wei, Ph.D. Computational Chemist Lorus Therapeutics Inc. 2 Meridian Road Toronto, On, M9W 4Z7 416-798-1200 Ext. 374 wwei(a)lorusthera.com This message contains CONFIDENTIAL INFORMATION intended solely for the us= e of the addressee(s) named above.=0AAny review, disclosure, distribution= , copying or use of the information by others is strictly prohibited. =0A= If you have received this message in error, please advise the sender by i= mmediate reply and delete the original message.=0A ------_=_NextPart_001_01C5A981.DE269300 Content-Type: text/HTML; charset="us-ascii" Content-Transfer-Encoding: quoted-printable X-NAIMIME-Disclaimer: 1 X-NAIMIME-Modified: 1 Hi all,

Could anybody suggest a software could c= onvert 3D structure file (.sd or .mol) to a 2D structure file for synthet= ic chemists reading?

Thanks in advance,
William

--------------------------------
William Wei, Ph.D.
Computational Chemist
Lorus Therapeutics Inc.
2 Meridian Road
Toronto, On, M9W 4Z7
416-798-1200 Ext. 374
wwei(a)lorusthera.com


This message contains CONFIDENTIAL INFORMATION intended solely for the us= e of the addressee(s) named above.
=0AAny review, disclosure, distribu= tion, copying or use of the information by others is strictly prohibited.=
=0AIf you have received this message in error, please advise the sen= der by immediate reply and delete the original message.
=0A

------_=_NextPart_001_01C5A981.DE269300-- From owner-chemistry@ccl.net Thu Aug 25 10:53:52 2005 From: "CCL" To: CCL Subject: CCL: study the bond's nature Message-Id: <-29001-050821034237-19981-uNy46x+EILo1kNckC1/Z/g-,-server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz-,-yahoo.fr] Hello, CCLers If you want to study ,theoreticaly, the nature(metallic, ionic, covalent...ext) of bonds in crystals or in molecules, what are the properties that you should calculate to fulfil this study? Thanks very much for your time. may abdelghani ___________________________________________________________________________ Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger Téléchargez cette version sur http://fr.messenger.yahoo.com From owner-chemistry@ccl.net Thu Aug 25 10:53:52 2005 From: "CCL" To: CCL Subject: CCL: When was Cheminformatics/Chemoinformatics used for the first time? Message-Id: <-29002-050823040317-26833-uNy46x+EILo1kNckC1/Z/g]~[server.ccl.net> X-Original-From: "W. Lingran Chen" Content-Type: multipart/alternative; boundary="------------020401060105040206030803" MIME-Version: 1.0 Sent to CCL by: "W. Lingran Chen" [lchen]~[mdli.com] This is a multi-part message in MIME format. --------------020401060105040206030803 Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit It is well-known that Cheminformatics/Chemoinformatics is a mimic of Bioinformatics. Does anyone know exactly when Cheminformatics/Chemoinformatics was used for the first time? -Lingran *********************************** William Lingran Chen, Ph.D. (a.k.a. Lingran Chen) Advisory Scientist Elsevier MDL 14600 Catalina Street San Leandro CA 94577 U.S.A. Phone: (510) 895-1313, x1305 FAX: (510) 614-3616 Email: L.Chen]~[mdl.com Web: www.elsevier.com www.mdl.com *********************************** --------------020401060105040206030803 Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit It is well-known that Cheminformatics/Chemoinformatics is a mimic of Bioinformatics.
Does anyone know exactly when Cheminformatics/Chemoinformatics was used for the first time?
-Lingran

***********************************
William Lingran Chen, Ph.D.
(a.k.a. Lingran Chen)
Advisory Scientist
Elsevier MDL
14600 Catalina Street
San Leandro
CA 94577
U.S.A.

Phone: (510) 895-1313, x1305
FAX:   (510) 614-3616

Email: L.Chen]~[mdl.com
Web:  www.elsevier.com
           www.mdl.com
***********************************

--------------020401060105040206030803-- From owner-chemistry@ccl.net Thu Aug 25 11:26:44 2005 From: "CCL" To: CCL Subject: CCL: octahedral coordination in Tinker Message-Id: <-29003-050825112417-18559-sJTYeKniThUXNerGpwThRw]^[server.ccl.net> X-Original-From: "Baltrusaitis, Jonas" content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Sent to CCL by: "Baltrusaitis, Jonas" Hi all, while working with GAMESS with integrated Tinker code, except other problems mentioned earlier, I found that Tinker doesn't recognize 6-fold coordination (octahedral). This problem was mentioned a while ago http://ccl.osc.edu/cgi-bin/ccl/message.cgi?2001+11+06+001 but there is no discussion given. Since I am a poor code changer (if anything) I can ask only CCL members. The GAMESS output is given below: XECUTION OF GAMESS BEGUN Thu Aug 25 09:54:08 2005 ECHO OF THE FIRST FEW INPUT CARDS - INPUT CARD> !Al14O22 test INPUT CARD> $CONTRL SCFTYP=RHF RUNTYP=optimize MULT=1 ICHARG=-2 NOSYM=1 INPUT CARD> COORD=TINKER NZVAR=114 UNITS=ANGS MAXIT=200 $END INPUT CARD> $BASIS GBASIS=N31 NGAUSS=6 NDFUNC=1 DIFFSP=.t. $END INPUT CARD> $GUESS GUESS=HUCKEL $END INPUT CARD> $intgrl qfmm=.f. $end INPUT CARD> $STATPT opttol= .0005 nprt=-2 npun=-1 NSTEP=200 HSSEND=.T. $END INPUT CARD> $ZMAT DLC=.T. AUTO=.T. $END INPUT CARD> $SCF DIRSCF=.T. NPUNCH=2 $END INPUT CARD> $SYSTEM TIMLIM=99999999 MEMORY=30000000 $END INPUT CARD> $TINXYZ INPUT CARD> 40 data MM2 parameters INPUT CARD> 1 Al -2.380900 4.123800 4.548300 1 9 12 13 INPUT CARD> 2 Al 2.369100 4.123800 4.548300 1 11 14 15 INPUT CARD> 3 Al 2.373000 1.374600 6.232900 2 7 8 10 14 INPUT CARD> 4 Al -2.380900 4.123800 8.389200 1 17 18 19 37 INPUT CARD> 5 Al 2.369100 4.123800 8.389200 1 8 20 21 39 INPUT CARD> 6 Al -0.003900 2.749200 6.704600 3 8 9 10 11 16 19 INPUT CARD> 7 O 3.820300 1.374600 7.546900 4 3 22 INPUT CARD> 8 O 1.647600 2.631000 7.546900 5 3 5 6 INPUT CARD> 9 O -1.451200 2.749200 5.390600 5 1 6 23 INPUT CARD> 10 O 0.721500 1.492700 5.390600 4 3 6 INPUT CARD> 11 O 0.718000 4.005600 5.390600 5 2 6 24 INPUT CARD> 12 O -1.659300 5.616500 5.390600 5 1 24 27 INPUT CARD> 13 O -4.032000 4.005600 5.390600 5 1 25 28 INPUT CARD> 14 O 3.298800 2.749200 5.390600 5 2 3 22 INPUT CARD> 15 O 3.090700 5.616500 5.390600 5 2 26 29 INPUT CARD> 16 O -0.929700 1.374600 7.546900 4 6 23 INPUT CARD> 17 O -3.310500 5.498300 7.546900 5 4 25 27 INPUT CARD> 18 O -3.102400 2.631000 7.546900 5 4 23 28 INPUT CARD> 19 O -0.729700 4.241900 7.546900 5 4 6 24 INPUT CARD> 20 O 1.439500 5.498300 7.546900 5 5 24 29 INPUT CARD> 21 O 4.020299 4.241900 7.546900 5 5 22 26 INPUT CARD> 22 Al 4.746100 2.749200 6.704600 2 7 14 21 33 INPUT CARD> 23 Al -2.377000 1.374600 6.232900 2 9 16 18 30 INPUT CARD> 24 Al -0.007800 5.498300 6.232900 3 11 12 19 20 31 34 INPUT CARD> 25 Al -4.757800 5.498300 6.232900 2 13 17 32 35 INPUT CARD> 26 Al 4.742200 5.498300 6.232900 2 15 21 33 36 INPUT CARD> 27 Al -2.384800 6.872900 6.704600 2 12 17 32 34 INPUT CARD> 28 Al -4.753900 2.749200 6.704600 2 13 18 30 35 INPUT CARD> 29 Al 2.365200 6.872900 6.704600 2 15 20 31 36 INPUT CARD> 30 O -4.028500 1.492700 5.390600 4 23 28 INPUT CARD> 31 O 0.918000 6.872900 5.390600 4 24 29 INPUT CARD> 32 O -3.832000 6.872900 5.390600 4 25 27 INPUT CARD> 33 O 5.468000 4.005600 5.390600 4 22 26 INPUT CARD> 34 O -0.733200 6.754800 7.546900 4 24 27 INPUT CARD> 35 O -5.479700 4.241900 7.546900 4 25 28 INPUT CARD> 36 O 4.016800 6.754800 7.546900 4 26 29 INPUT CARD> 37 O -1.054577 4.218151 10.639080 4 4 38 INPUT CARD> 38 C 0.132575 4.310390 11.356130 6 37 39 40 ..... DONE SETTING UP THE RUN ..... ---- QMMM procedure is ON ---- ############################################################################## ############################################################################## ## ## ## TINKER --- Software Tools for Molecular Design ## ## ## ## Version 3.6 February 1998 ## ## ## ## Copyright (c) Jay William Ponder 1990-1998 ## ## All Rights Reserved ## ## ## ############################################################################## ############################################################################## READXYZ -- Check Connection of Atom 6 to Atom 16 TINKER is Unable to Continue; Terminating the Current Calculation ddikick.exe: application process 0 quit unexpectedly. From owner-chemistry@ccl.net Thu Aug 25 12:03:23 2005 From: "CCL" To: CCL Subject: CCL: ESP grid in Gaussian without QM? Message-Id: <-29004-050825113130-23825-sJTYeKniThUXNerGpwThRw]![server.ccl.net> X-Original-From: Anselm.Horn]![chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: Anselm.Horn]![chemie.uni-erlangen.de Dear all, a Gaussian question: Is it possible to print out the electrostatic potential grid used for population analysis e.g. via pop=MK iop(6/33=2) iop(6/42=6) without performing any QM calculation, i.e. use the Gaussian program as plain grid creator? I tried to run an MM calculation with the above keywords, but that failed. In my case, the molecule of interest is rather large, so any QM calculation is not feasible. Best regards, Anselm Horn From owner-chemistry@ccl.net Thu Aug 25 12:55:09 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-29005-050825112751-20419-sJTYeKniThUXNerGpwThRw]-[server.ccl.net> X-Original-From: Aaron Deskins Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed MIME-Version: 1.0 Sent to CCL by: Aaron Deskins CCL wrote: > > Sent to CCL by: "Mgr. Lubos Vrbka" > >> Why not put a gold slab thru the middle, and use standard 3D PBC? You >> get twice the surface area that way as well. > > in this case it would be probably better to use 3D PBC with slab > correction to ewald summation provided by gromacs (type 3dbc). > i think this will provide better results than 2D PBC that are very > computationally inefficient (when compared to 3D) > dlpoly package provides true "slab" PBC. i'm not sure how the > long-range electrostatics is handled in this case, though. > What method would you use to describe the forces/energies of the periodic structure? My (limited) understanding is that many semi-emperical methods (like AM1, etc.) don't do so well at describing 3d periodic structures. How about the empirical force field methods (CHARMM, etc.)? Do they work? I only am aware of a few empirical/semi-empirical methods (MEAM - modified embedded atom method, tight-binding) that have been used to model surfaces, and getting adsorbate/surface interaction parameters seems like a real chore. Of course more robust DFT programs (VASP, Dacapo, etc.) are regularly used to model surfaces, but are computationally-intensive. If anyone can give some valid empirical/semi-empirical theories/methods to model 3d periodic structures, your help is appreciated. Thank you, Aaron Deskins Purdue University From owner-chemistry@ccl.net Thu Aug 25 13:37:57 2005 From: "CCL" To: CCL Subject: CCL: Castep-PDOS Message-Id: <-29007-050824050205-8550-sJTYeKniThUXNerGpwThRw]|[server.ccl.net> X-Original-From: "serdar durdagi" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: "serdar durdagi" [durdagi]|[fhi-berlin.mpg.de] Hi, In my calculations, I am using CASTEP. Does anybody knows, how can I plot PDOS from pdos_weights file. It is a binary file. Thank you very much. Serdar Durdagi -------------------------------------------------- Serdar Durdagi, M.Sc. Ph.D. student Theory Department, Fritz-Haber-Institute of Max-Planck Society Faradayweg, 4-6, Berlin-Dahlem, D-14195,Germany Tel: +49-30-8413-4844 (office) +49-162-201-3631 (mobile) -------------------------------------------------- From owner-chemistry@ccl.net Thu Aug 25 14:17:01 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-29008-050825135828-26570-sJTYeKniThUXNerGpwThRw]|[server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable]|[pollux.cber.nih.gov] On Thu, 25 Aug 2005, CCL wrote: > > Sent to CCL by: "Mgr. Lubos Vrbka" > > > >> Why not put a gold slab thru the middle, and use standard 3D PBC? You > >> get twice the surface area that way as well. > > > > in this case it would be probably better to use 3D PBC with slab > > correction to ewald summation provided by gromacs (type 3dbc). > > i think this will provide better results than 2D PBC that are very > > computationally inefficient (when compared to 3D) > > dlpoly package provides true "slab" PBC. i'm not sure how the > > long-range electrostatics is handled in this case, though. Since the question topic was "molecular dynamics" I was assuming a package such as CHARMM, AMBER, NAMD, GROMOS, TINKER, etc., most of which do fairly well at describing periodic structures, esp. for the 3D case. Details such as system height, slab thickess, etc. would need to be optimized, but it's a reasonable option, esp. if 2D PBC aren't readily available. OTOH, the water:gold interaction might be tricky to get right with a simple point charge based potential; a polarizable potential might be a better choice. > Sent to CCL by: Aaron Deskins > CCL wrote: > What method would you use to describe the forces/energies of the > periodic structure? > > My (limited) understanding is that many semi-emperical methods (like > AM1, etc.) don't do so well at describing 3d periodic structures. How > about the empirical force field methods (CHARMM, etc.)? Do they work? I > only am aware of a few empirical/semi-empirical methods (MEAM - modified > embedded atom method, tight-binding) that have been used to model > surfaces, and getting adsorbate/surface interaction parameters seems > like a real chore. > > Of course more robust DFT programs (VASP, Dacapo, etc.) are regularly > used to model surfaces, but are computationally-intensive. > > If anyone can give some valid empirical/semi-empirical theories/methods > to model 3d periodic structures, your help is appreciated. ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable]|[nih.gov ALT email: rvenable]|[speakeasy.org ------------------------------------- nekcihC toboR From owner-chemistry@ccl.net Thu Aug 25 14:19:51 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-29009-050825135828-26570-sJTYeKniThUXNerGpwThRw-.-server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable-.-pollux.cber.nih.gov] On Thu, 25 Aug 2005, CCL wrote: > > Sent to CCL by: "Mgr. Lubos Vrbka" > > > >> Why not put a gold slab thru the middle, and use standard 3D PBC? You > >> get twice the surface area that way as well. > > > > in this case it would be probably better to use 3D PBC with slab > > correction to ewald summation provided by gromacs (type 3dbc). > > i think this will provide better results than 2D PBC that are very > > computationally inefficient (when compared to 3D) > > dlpoly package provides true "slab" PBC. i'm not sure how the > > long-range electrostatics is handled in this case, though. Since the question topic was "molecular dynamics" I was assuming a package such as CHARMM, AMBER, NAMD, GROMOS, TINKER, etc., most of which do fairly well at describing periodic structures, esp. for the 3D case. Details such as system height, slab thickess, etc. would need to be optimized, but it's a reasonable option, esp. if 2D PBC aren't readily available. OTOH, the water:gold interaction might be tricky to get right with a simple point charge based potential; a polarizable potential might be a better choice. > Sent to CCL by: Aaron Deskins > CCL wrote: > What method would you use to describe the forces/energies of the > periodic structure? > > My (limited) understanding is that many semi-emperical methods (like > AM1, etc.) don't do so well at describing 3d periodic structures. How > about the empirical force field methods (CHARMM, etc.)? Do they work? I > only am aware of a few empirical/semi-empirical methods (MEAM - modified > embedded atom method, tight-binding) that have been used to model > surfaces, and getting adsorbate/surface interaction parameters seems > like a real chore. > > Of course more robust DFT programs (VASP, Dacapo, etc.) are regularly > used to model surfaces, but are computationally-intensive. > > If anyone can give some valid empirical/semi-empirical theories/methods > to model 3d periodic structures, your help is appreciated. ------------------------------------- Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable-.-nih.gov ALT email: rvenable-.-speakeasy.org ------------------------------------- nekcihC toboR From owner-chemistry@ccl.net Thu Aug 25 15:23:04 2005 From: "CCL" To: CCL Subject: CCL: Molecular dynamics w/ 2D PBC Message-Id: <-29010-050825134050-21144-sJTYeKniThUXNerGpwThRw/a\server.ccl.net> X-Original-From: "Ozgur YAZAYDIN" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: "Ozgur YAZAYDIN" [yazaydin/a\WPI.EDU] > I want to run a MD calculation of water molecules on a gold surface > using > 2D periodic boundary conditions. Does anobody knows a program that can do > it, painless? > Thanks in advance. > João Otávio M. A. Lins DL_POLY simulation package is capable of handling 2D simulations by calculating electrostatic forces with Hautman Klein Ewald (HKE) method. The only limitation is that; length of the non periodic direction of your simulation box should be significantly smaller than the length of the periodic directions. For example, if you place your gold-water interface on the xy plane and you have periodicity for the x and y directions and non-periodicity for the z direction then Lx >> Lz and Ly >> Lz. http://www.cse.clrc.ac.uk/msi/software/DL_POLY/ Otherwise your only practical option is to place a vacuum around your slab in the direction you want non periodicity so that new simulation box is at least 5 times longer than your original simulation box. You can do it so using DL_POLY too. -- Ozgur YAZAYDIN Research Assistant Department of Chemical Engineering Worcester Polytechnic Institute 100 Institute Rd. Worcester, MA 01609-2280 USA "I want to know God's thoughts... ... the rest are details" Albert Einstein From owner-chemistry@ccl.net Thu Aug 25 20:25:30 2005 From: "CCL" To: CCL Subject: CCL: Message from CCL Admin: changes and explanations Message-Id: <-29011-050825184115-32369-sJTYeKniThUXNerGpwThRw[a]server.ccl.net> X-Original-From: janl[a]speakeasy.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Sent to CCL by: janl[a]speakeasy.net Dear CCL, I am back from my 7 week travels and trying to cope with the backlog. I am sorry that some things were not working as they should during my absence, but I'd rather have it secure than easy, since I was not able to monitor CCL during my absence from home. The good news is that looking through the security logs I did not find any compromise of CCL computers and spam did not appear on CCL in large quantity. The bad news is that some of you lost patience with my confirmation scripts and abandoned their messages. I am working on bugs/improvements now... Sorry for some mishaps in the past few days. Bear with me... Few bullets: - For the next few days I will be changing a lot of things on CCL and you will be victims of occasional junk mail or repeated messages. Sorry... - I am currently self-employed. The CCL ran for half a year from my own computers from my home. To keep CCL running I will have to develop some way of supporting it and my time spent for CCL. Non-intrusive advertising is the simplest venue. I want to develop services that will not affect the free distribution of CCL and free access to its web site. I want these services to be useful for the subscribers too... Initially, I want to charge for job openings ads. More about it, in next messages... CCL will be run initially as a for-profit LLC or Corporation. Why? I will tell you more later, but in short: "I do not want to have conflict of interest and a lot of red tape". I will gladly change to 501(c)3 if CCL generates enough income. - I will be sending (in small pieces, as I go) explanations of some technical issues/changes with CCL, rather than do it in one message. This will allow me to test new distribution scripts and other pieces of software that runs CCL and tries to do it securely. Please bear with me and please glance at this stuff, so you can use CCL better and more efficient. When I am finished, I will put this stuff on the web. It is long overdue, but for the past two years, I really did not have much sleep and CCL had to run in the basic maintenance mode. Jan Labanowski CCL Manager jkl[a]ccl.net From owner-chemistry@ccl.net Thu Aug 25 20:52:35 2005 From: "CCL" To: CCL Subject: CCL: Software convert 3D structure .sd file to 2D structure Message-Id: <-29014-050825125119-26616-sJTYeKniThUXNerGpwThRw]*[server.ccl.net> X-Original-From: "RMC Biosciences, Inc." Content-Type: multipart/related; boundary="----=_NextPart_000_0111_01C5A95B.B0F60B40"; type="multipart/alternative" MIME-Version: 1.0 Sent to CCL by: "RMC Biosciences, Inc." [rcasey]*[rmcbiosciences.com] This is a multi-part message in MIME format. ------=_NextPart_000_0111_01C5A95B.B0F60B40 Content-Type: multipart/alternative; boundary="----=_NextPart_001_0112_01C5A95B.B0F60B40" ------=_NextPart_001_0112_01C5A95B.B0F60B40 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Software convert 3D structure .sd file to 2D structureWilliam, You might want to check the products and toolkits offered by OpenEye = Scientific Software (www.eyesopen.com). They have several packages that = convert structure files. Also, OpenBabel = http://openbabel.sourceforge.net/ has various conversion routines. Hope = this helps...... Regards, Richard Casey, PhD Partners in Drug Discovery=20 =20 RMC Biosciences, Inc. 912 E. Ridgecrest Road Fort Collins, CO 80524 =20 rcasey]*[rmcbiosciences.com www.rmcbiosciences.com tel:=20 fax:=20 mobile: 970-224-0456 970-224-2831 970-980-5975 =20 =20 =20 =20 =20 Add me to your address book... Want a signature like this?=20 =20 ----- Original Message -----=20 From: CCL=20 To: Casey, Richard =20 Sent: Thursday, August 25, 2005 8:38 AM Subject: CCL: Software convert 3D structure .sd file to 2D structure Hi all,=20 Could anybody suggest a software could convert 3D structure file (.sd = or .mol) to a 2D structure file for synthetic chemists reading? Thanks in advance,=20 William=20 --------------------------------=20 William Wei, Ph.D.=20 Computational Chemist=20 Lorus Therapeutics Inc.=20 2 Meridian Road=20 Toronto, On, M9W 4Z7=20 416-798-1200 Ext. 374=20 wwei]*[lorusthera.com=20 -------------------------------------------------------------------------= ----- This message contains CONFIDENTIAL INFORMATION intended solely for the = use of the addressee(s) named above. Any review, disclosure, distribution, copying or use of the = information by others is strictly prohibited.=20 If you have received this message in error, please advise the sender = by immediate reply and delete the original message. ------=_NextPart_001_0112_01C5A95B.B0F60B40 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Software convert 3D structure .sd file to 2D = structure
William,
 
You might want to check the products = and toolkits=20 offered by OpenEye Scientific Software (www.eyesopen.com).  They have = several=20 packages that convert structure files. Also,=20 OpenBabel http://openbabel.sourceforge.n= et/ has=20 various conversion routines.  Hope this helps......
 
 
Regards,
Richard Casey, PhD
 
 
Partners in Drug=20 Discovery
RMC Biosciences, Inc. 912 E. Ridgecrest Road
Fort = Collins, CO=20 80524
rcasey]*[rmcbiosciences.com
www.rmcbiosciences.com
tel: =
fax:=20
mobile: 		970-224-0456
970-224-2831
970-980-5975=20 =
Add me to your address = book... Want a signature like=20 = this?
----- Original Message -----
From:=20 CCL=20
Sent: Thursday, August 25, 2005 = 8:38=20 AM
Subject: CCL: Software convert = 3D=20 structure .sd file to 2D structure

Hi all,

Could anybody suggest a software could = convert 3D=20 structure file (.sd or .mol) to a 2D structure file for synthetic = chemists=20 reading?

Thanks in advance,
William

-------------------------------- =
William Wei, Ph.D.
Computational Chemist
Lorus=20 Therapeutics Inc.
2 Meridian = Road=20
Toronto, On, M9W 4Z7
416-798-1200 Ext. 374
wwei]*[lorusthera.com =


This message contains CONFIDENTIAL INFORMATION intended solely for the = use of=20 the addressee(s) named above.
Any review, disclosure, distribution, = copying=20 or use of the information by others is strictly prohibited.
If you = have=20 received this message in error, please advise the sender by immediate = reply=20 and delete the original message.

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Message-Id: <-29013-050825083455-15505-sJTYeKniThUXNerGpwThRw.:.server.ccl.net> X-Original-From: peter ryan Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 MIME-Version: 1.0 Sent to CCL by: peter ryan [ryanp.:.tcd.ie] Hi all I have been using Dmol 3 to examine reaction profiles for some organic molecules on the Silicon 100 surface in a peiodic regime. With Dmol you have the option of creating 3D plots of DFT molecular orbitals in the molecular case and periodic case. Computation of orbitals is possible for molecules and for periodics that use the Gamma-point, but not for periodic cases with multiple k-points. Is there any way to examine the molecular orbitals for periodics at K points other than the gamma point...specifically the HOMO and LUMO levels at other K points. Or does anyone know of some program that may facilate this analysis.. thanking you all in advance. Peter Ryan SFI Boland Lab Chemistry Dept. Trinity College Dublin. College Green Dublin 2 phone +353 (0)1 6083143 From owner-chemistry@ccl.net Thu Aug 25 20:52:36 2005 From: "CCL" To: CCL Subject: CCL: GAMESS restart Message-Id: <-29017-050823131616-28822-sJTYeKniThUXNerGpwThRw^_^server.ccl.net> X-Original-From: "William Wei" content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C5A7FF.C8E1C80A" MIME-Version: 1.0 Sent to CCL by: "William Wei" [wwei^_^lorusthera.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C5A7FF.C8E1C80A Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable Hi Fellows, I just started to use GAMESS for a structure optimixation. Because the time and MAXIT issue, GAMESS stopped without writing coordinates(at least I did not find). So I am wondering that what option I need to use for restart GAMESS with my geometry optimization? There is a ./scr/.dat file in my home directory. Anybody could help me to restart the job? Thanks in advance, William -------------------------------- William Wei, Ph.D. Computational Chemist Lorus Therapeutics Inc. 2 Meridian Road Toronto, On, M9W 4Z7 416-798-1200 Ext. 374 wwei^_^lorusthera.com ------_=_NextPart_001_01C5A7FF.C8E1C80A Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable GAMESS restart

Hi Fellows,

I just started to use GAMESS for a = structure optimixation.  Because the time and MAXIT issue, GAMESS = stopped without writing  coordinates(at least I did not find). So I = am wondering that what option I need to use for restart GAMESS with my = geometry optimization?   There is a ./scr/.dat file in my home = directory.  Anybody could help me to restart the job?

Thanks in advance,
William

--------------------------------
William Wei, Ph.D.
Computational Chemist
Lorus Therapeutics Inc.
2 Meridian Road
Toronto, On, M9W 4Z7
416-798-1200 Ext. 374
wwei^_^lorusthera.com


------_=_NextPart_001_01C5A7FF.C8E1C80A-- From owner-chemistry@ccl.net Thu Aug 25 20:52:35 2005 From: "CCL" server.ccl.net> To: CCL Subject: CCL: W:GAMESS input question Message-Id: <-29015-050824152536-8157-sJTYeKniThUXNerGpwThRw<*>server.ccl.net> X-Original-From: "Tony Yuan" camsoft.com> Sent to CCL by: "Tony Yuan" [tyuan<*]camsoft.com> Can more than 1 ORIGIN(i), XVEC(i) and YVEC(i) be set in GRID group? If yes, how to set? A sample will be very appreciated. I tried following format: INPUT CARD> GRID INPUT CARD>ORIGIN(1)=0.0, 0.0, 1.0 INPUT CARD>XVEC(1)=2.0, 0.0, 1.0 INPUT CARD>YVEC(1)=0.0, 2.0, 1.0 INPUT CARD>ORIGIN(2)=0.0, 0.0, 1.1 INPUT CARD>XVEC(2)=2.0, 0.0, 1.1 INPUT CARD>YVEC(2)=0.0, 2.0, 1.1 INPUT CARD>SIZE=0.2 INPUT CARD>UNITS=ANGS INPUT CARD> END It doesnt work. Sincerely -Tony From owner-chemistry@ccl.net Thu Aug 25 20:52:35 2005 From: "CCL" To: CCL Subject: CCL: G03 ECP silver atoms Message-Id: <-29016-050824071532-14798-sJTYeKniThUXNerGpwThRw:_:server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz:_:yahoo.fr] Hello, CCLers When I decided to constructed a ECP for Ag2 in G03 software I recognize this problem: in term of this error message: QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE. ' Last state="Top" TCursr= 879 LCursr= 0 Error reading general basis specification. I hop that you can help me to correct my input: %chk=Ag2.chk %mem=6MW %nproc=1 # b3pw91 gen pseudo=read test Ag2 0 1 Ag Ag 1 B1 B1 2.68019104 Ag 0 OLP 3 28 f 5 0 568.700624 -0.587930000E-01 1 162.357907 -20.1145146 2 51.1025755 -104.273311 2 16.9205822 -40.4539787 2 6.16695960 -3.44200090 s-f 5 0 76.0974658 2.98615270 1 15.3327359 35.1576460 2 18.7715345 450.180991 2 13.3663294 -866.024831 2 9.82369480 523.111018 p-f 5 0 56.3318043 4.96406710 1 69.0609098 21.5028219 2 19.2717998 546.027545 2 12.5770654 -600.382256 2 8.79566700 348.294929 d-f 5 0 53.4641078 3.04674860 1 40.1975457 23.3656705 2 11.9086073 777.254012 2 9.75281830 -1238.86024 2 8.17889970 608.067712 ___________________________________________________________________________ Appel audio GRATUIT partout dans le monde avec le nouveau Yahoo! Messenger Téléchargez cette version sur http://fr.messenger.yahoo.com From owner-chemistry@ccl.net Thu Aug 25 20:52:35 2005 From: "CCL" To: CCL Subject: CCL: molecular orbitals for multiple K points ? Message-Id: <-29012-050825094927-28701-sJTYeKniThUXNerGpwThRw{=}server.ccl.net> X-Original-From: Peter Ryan Content-Type: TEXT/PLAIN; charset=US-ASCII MIME-Version: 1.0 Sent to CCL by: Peter Ryan [poiuyt{=}maths.tcd.ie] Hi all I have been using Dmol 3 to examine reaction profiles for some organic molecules on the Silicon 100 surface in a peiodic regime. With Dmol you have the option of creating 3D plots of DFT molecular orbitals in the molecular case and periodic case. Computation of orbitals is possible for molecules and for periodics that use the Gamma-point, but not for periodic cases with multiple k-points. Is there any way to examine the molecular orbitals for periodics at K points other than the gamma point...specifically the HOMO and LUMO levels at other K points. Or does anyone know of some program that may facilate this analysis.. thanking you all in advance. Peter Ryan SFI Boland Lab Chemistry Dept. Trinity College Dublin. College Green Dublin 2 phone +353 (0)1 6083143 From owner-chemistry@ccl.net Thu Aug 25 22:21:32 2005 From: "CCL" To: CCL Subject: CCL: 06.03.26 Spring ACS: Interactions of Peptides and Proteings with Membrane Surfaces Message-Id: <-29018-050825161527-1234-sJTYeKniThUXNerGpwThRw|"|server.ccl.net> X-Original-From: Themis Lazaridis Content-Type: multipart/alternative; boundary=Apple-Mail-13-488433257 Mime-Version: 1.0 Sent to CCL by: Themis Lazaridis [tlazaridis|"|sci.ccny.cuny.edu] --Apple-Mail-13-488433257 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=WINDOWS-1252; format=flowed Hi. Could you please post this announcement on CCL? Thanks! --- Themis Lazaridis Associate Professor phone (212) 650-8364 Department of Chemistry fax (212) 650-6107 City College of New York / CUNY email: tlazaridis|"|ccny.cuny.edu Convent Avenue & 138th St. = http://www.sci.ccny.cuny.edu/~themis New York, NY 10031 http://mingus.sci.ccny.cuny.edu Dear all, We would like to let you know of an upcoming symposium on =93Interactions=20= of Peptides and Proteins with Membrane Surfaces=94 at the Spring 2006=20 National American Chemical Society Meeting, March 26-30 in Atlanta,=20 Georgia. A brief summary of the intent and purpose of the symposium is as=20 follows: "The adsorption of peripheral proteins and peptides to membranes plays=20= an important role in many biological processes. The interplay of many=20 factors, including the alteration of the biophysical properties of the=20= macromolecules upon association and their consequent lateral=20 reorganization at the membrane surface, presents exciting challenges to=20= biophysicists and biochemists. Obtaining a molecular-level=20 understanding of the physico-chemical forces that drive and regulate=20 protein/membrane interactions therefore requires the integration of=20 diverse approaches. The goal of this symposium is to bring together=20 leading experimentalists and theorists in this field whose research=20 addresses these issues in novel and creative ways. Emphasis will be=20 placed on how theory and experiment may be combined to provide more=20 comprehensive and detailed information on protein/membrane systems than=20= is attainable from one perspective alone and, thus, lead to new models=20= and hypotheses." It will be a full, 4-day symposium. The list of confirmed speakers is=20= at the end of this message. Unfortunately, the limits set by ACS did=20 not allow us to invite everyone we had in mind. However, additional=20 speakers will be selected from the submitted abstracts, so please=20 consider sending one. And, of course, there will be plenty of room for=20= posters. All the best, Themis Lazaridis City College of New York / CUNY tlazaridis|"|ccny.cuny.edu, 212-650-8364 and Diana Murray Weill Medical College of Cornell University dim2007|"|med.cornell.edu, 212-746-1184 Confirmed Speakers Paul Axelsen, U Penn Charles Brooks III, Scripps David Cafiso, U Virginia Wonhwa Cho, U Illinois Rosemary Cornell, Simon Fraser University Ben de Kruijff, Utrecht U William DeGrado, U Pennsylvania Eric Freed, NCI Michael Gelb, U Washington Jay Groves, Berkeley Volkhard Helms, Denmark Blake Hill, Johns Hopkins Huey Huang, Rice U Tatiana Kutateladze, U Colorado Sylvio May, Friedrich-Schiller-UniversityB Ole Mouritsen, Denmark Mary Roberts, Boston College Mark Sansom, Oxford Yechiel Shai, Weizmann Institute Lukas Tamm, U. Virginia Suren A. Tatulian, U Central Florida Doug Tobias/Ryan Benz, UC Irvine Nancy Thompson, U North Carolina Peter Tieleman, U Calgary Volker Vogt, Cornell Steve White, UC Irvine Tuck Wong, U Missouri Tom Woolf, Johns Hopkins= --Apple-Mail-13-488433257 Content-Transfer-Encoding: quoted-printable Content-Type: text/enriched; charset=WINDOWS-1252 Hi. Could you please post this announcement on CCL?=20 Thanks! --- Themis Lazaridis Associate Professor phone (212) 650-8364 Department of Chemistry fax (212) 650-6107 City College of New York / CUNY email: tlazaridis|"|ccny.cuny.edu Convent Avenue & 138th St. = http://www.sci.ccny.cuny.edu/~themis New York, NY 10031 http://mingus.sci.ccny.cuny.edu TimesDear all, We would like to let you know of an upcoming symposium on =93Interactions of Peptides and Proteins with Membrane Surfaces=94 at = the Spring 2006 National American Chemical Society Meeting, March 26-30 in Atlanta, Georgia.=20 A brief summary of the intent and purpose of the symposium is as follows:=20 "The adsorption of peripheral proteins and peptides to membranes plays an important role in many biological processes. The interplay of many factors, including the alteration of the biophysical properties of the macromolecules upon association and their consequent lateral reorganization at the membrane surface, presents exciting challenges to biophysicists and biochemists. Obtaining a molecular-level understanding of the physico-chemical forces that drive and regulate protein/membrane interactions therefore requires the integration of diverse approaches. The goal of this symposium is to bring together leading experimentalists and theorists in this field whose research addresses these issues in novel and creative ways. Emphasis will be placed on how theory and experiment may be combined to provide more comprehensive and detailed information on protein/membrane systems than is attainable from one perspective alone and, thus, lead to new models and hypotheses."=20 It will be a full, 4-day symposium. The list of confirmed speakers is at the end of this message. Unfortunately, the limits set by ACS did not allow us to invite everyone we had in mind. However, additional speakers will be selected from the submitted abstracts, so please consider sending one. And, of course, there will be plenty of room for posters.=20 All the best,=20 Themis Lazaridis=20 City College of New York / CUNY=20 0000,0000,EEEAtlazaridis|"|ccny.cuny.edu, 212-650-8364=20 and=20 Diana Murray=20 Weill Medical College of Cornell University=20 0000,0000,EEEAdim2007|"|med.cornell.edu, 212-746-1184=20 Confirmed Speakers Paul Axelsen, U Penn Charles Brooks III, Scripps David Cafiso, U Virginia Wonhwa Cho, U Illinois Rosemary Cornell, Simon Fraser University Ben de Kruijff, Utrecht U William DeGrado, U Pennsylvania Eric Freed, NCI Michael Gelb, U Washington Jay Groves, Berkeley Volkhard Helms, Denmark Blake Hill, Johns Hopkins Huey Huang, Rice U Tatiana Kutateladze, U Colorado Sylvio May, Friedrich-Schiller-UniversityB Ole Mouritsen, Denmark Mary Roberts, Boston College Mark Sansom, Oxford Yechiel Shai, Weizmann Institute Lukas Tamm, U. Virginia Suren A. Tatulian, U Central Florida Doug Tobias/Ryan Benz, UC Irvine Nancy Thompson, U North Carolina Peter Tieleman, U Calgary Volker Vogt, Cornell Steve White, UC Irvine Tuck Wong, U Missouri Tom Woolf, Johns Hopkins= --Apple-Mail-13-488433257--