From owner-chemistry@ccl.net Fri May 19 00:08:00 2006 From: "Sidney Ramos Santana santanasidney-.-yahoo.com.br" To: CCL Subject: CCL: Converting XYZ to VRML Version 2.0 Message-Id: <-31787-060518211451-11859-E9O266xzYOANkHnwB4ppQg[*]server.ccl.net> X-Original-From: "Sidney Ramos Santana" Date: Thu, 18 May 2006 21:14:50 -0400 Sent to CCL by: "Sidney Ramos Santana" [santanasidney\a/yahoo.com.br] Dear CCL Users, I am needing to convert a XYZ file to VRML file (Version 2.0) than can be read in the Octaga Player. Do you know any program (free) than can do this ? What kind of intructions I can write in a fortran file to create a filter to do this task? Please, could anyone help me? Best Regards, Sidney Ramos Santana Computational Chemistry Laboratory - LQC Graduate Program of Materials Science - PGMTR Fundamental Chemistry Department - DQF Federal University of Pernambuco - UFPE Recife - Brazil email: santanasidney_at_yahoo.com.br From owner-chemistry@ccl.net Fri May 19 03:46:00 2006 From: "Wolf-D. Ihlenfeldt wdi..xemistry.com" To: CCL Subject: CCL: Converting XYZ to VRML Version 2.0 Message-Id: <-31788-060519023805-28185-SDmXg4waXONCGSOANS/uoQ%x%server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 19 May 2006 01:37:50 -0400 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi|xemistry.com] That can be easily done with a very simple CACTVS script (www.xemistry.com/academic): Run as "csts -f scriptfile.tcl" --- scriptfile.tcl --- # read a structure from an xyz file set eh [molfile read yourfile.xyz] # set few parameters for the display style, output file name, etc. prop setparam E_VRML filename yourfile.vrml style ballstick # create the file ens get $eh E_VRML # cleanup ens delete all ------- W. D. Ihlenfeldt Xemistry GmbH wdi(a)xemistry.com > -----Original Message----- > From: owner-chemistry(a)ccl.net [mailto:owner-chemistry(a)ccl.net] > Sent: Friday, May 19, 2006 12:20 AM > To: Ihlenfeldt, W.d. > Subject: CCL: Converting XYZ to VRML Version 2.0 > > Sent to CCL by: "Sidney Ramos Santana" > [santanasidney\a/yahoo.com.br] Dear CCL Users, > > > I am needing to convert a XYZ file to VRML file (Version 2.0) > than can be read in the Octaga Player. > Do you know any program (free) than can do this ? > > What kind of intructions I can write in > a fortran file to create a filter to do this task? > > Please, could anyone help me? > > Best Regards, > > Sidney Ramos Santana > Computational Chemistry Laboratory - LQC Graduate Program of > Materials Science - PGMTR Fundamental Chemistry Department - > DQF Federal University of Pernambuco - UFPE Recife - Brazil > email: santanasidney_at_yahoo.com.br > > > > -= 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.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > From owner-chemistry@ccl.net Fri May 19 05:26:00 2006 From: "Ramon Crehuet rcsqtc..iiqab.csic.es" To: CCL Subject: CCL: Parameters for PCM calculation Message-Id: <-31789-060519043454-27570-lYbOOKSZP67eF+mz2IbF+A||server.ccl.net> X-Original-From: Ramon Crehuet Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 19 May 2006 09:37:59 +0200 MIME-Version: 1.0 Sent to CCL by: Ramon Crehuet [rcsqtc.:.iiqab.csic.es] Dear CCLers, I would like to do a PCM calculation using GAMESS and this program needs some parameters for the solvent. I guess any software needs this parameters. Ideally I should use olive oil as solvent, but ether has a similar dielectric constant. Precisely I don't know where to find the following properties: * the solvent radius * the thermal expansion coefficient * the thermal coefficient of the surface tenstion * the cavity microscopic coefficient * solvent numeral density * distances between the first atoms of each type and the cavity (can this be just a guess or should this be calculated? And how?) I have the feeling that usually only water is used as a solvent and that although the method in GAMESS is general, the solvent parameters for other solvents are not trivial and,thus, other solvents are rarely used. Has anybody experience with that? Thanks for your attention, Ramon Crehuet From owner-chemistry@ccl.net Fri May 19 06:25:00 2006 From: "Andreas Klamt klamt---cosmologic.de" To: CCL Subject: CCL: Parameters for PCM calculation Message-Id: <-31790-060519062248-25390-MKOnjLcvikrgO1t75/TkYQ:-:server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15 Date: Fri, 19 May 2006 12:22:39 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt*_*cosmologic.de] Dear Ramon, you are right: almost all implicit solvation models are parameterized mainly for water and have a crude scaling for lower dielectric constants. You cannot expect that the specific details of a solvent as olive oil is reasonably quantitatively described by such implicit solvation method. I personally consider the change of te solvent radius according to the solvent as a very unphysical concept, and I doubt that there are any good rules how to set that radius. As far as I know, the only implicit solvation method that can deal with almost arbitrary solvent and solvents mixtures, even at variable temperatures without the need for any solvent information (not even the dielectric constant) is my COSMO-RS method. COSMO-RS describes solutes and solvents on the same quantum-chemical footing and brings them together by a statistical thermodynamics of interacting surfaces. For more details and lots of references see our homepage or my book "COSMO-RS: From quantum chemistry to fluid phase thermodynamics and drug design", Elsevier, 2005. Regards Andreas Ramon Crehuet rcsqtc..iiqab.csic.es schrieb: > Sent to CCL by: Ramon Crehuet [rcsqtc.:.iiqab.csic.es] > Dear CCLers, > I would like to do a PCM calculation using GAMESS and this program needs > some parameters for the solvent. I guess any software needs this > parameters. Ideally I should use olive oil as solvent, but ether has a > similar dielectric constant. > Precisely I don't know where to find the following properties: > * the solvent radius > * the thermal expansion coefficient > * the thermal coefficient of the surface tenstion > * the cavity microscopic coefficient > * solvent numeral density > * distances between the first atoms of each type and the cavity (can > this be just a guess or should this be calculated? And how?) > > I have the feeling that usually only water is used as a solvent and that > although the method in GAMESS is general, the solvent parameters for > other solvents are not trivial and,thus, other solvents are rarely used. > Has anybody experience with that? > Thanks for your attention, > Ramon Crehuet> > > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt(!)cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Fri May 19 07:50:00 2006 From: "John McKelvey jmmckel%a%attglobal.net" To: CCL Subject: CCL: Parameters for PCM calculation Message-Id: <-31791-060519073033-18537-JZnyi3qFLczR9KNSDtkp5A++server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 19 May 2006 07:22:58 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel##attglobal.net] Hello.. My $0.02.... I'm quite interested in solvation effects for TDDFT, and find the article in JACS, V128,p2072-2083 (2006) somewhat pertinent to this discussion. It deals with TDDFT/PCM with various solvent [and their respective radii], and I find the results extremely interesting... maybe even stunning in terms of accuracy for albeit a rather closed set of example molecular structures.. Cheers, John McKelvey Andreas Klamt klamt---cosmologic.de wrote: >Sent to CCL by: Andreas Klamt [klamt*_*cosmologic.de] >Dear Ramon, > >you are right: almost all implicit solvation models are parameterized >mainly for water and have a crude scaling for lower dielectric >constants. You cannot expect that the specific details of a solvent as >olive oil is reasonably quantitatively described by such implicit >solvation method. I personally consider the change of te solvent radius >according to the solvent as a very unphysical concept, and I doubt that >there are any good rules how to set that radius. > >As far as I know, the only implicit solvation method that can deal with >almost arbitrary solvent and solvents mixtures, even at variable >temperatures without the need for any solvent information (not even the >dielectric constant) is my COSMO-RS method. COSMO-RS describes solutes >and solvents on the same quantum-chemical footing and brings them >together by a statistical thermodynamics of interacting surfaces. > >For more details and lots of references see our homepage or my book >"COSMO-RS: From quantum chemistry to fluid phase thermodynamics and drug >design", Elsevier, 2005. > >Regards > >Andreas > > >Ramon Crehuet rcsqtc..iiqab.csic.es schrieb: > > >>Sent to CCL by: Ramon Crehuet [rcsqtc.:.iiqab.csic.es] >>Dear CCLers, >>I would like to do a PCM calculation using GAMESS and this program needs >>some parameters for the solvent. I guess any software needs this >>parameters. Ideally I should use olive oil as solvent, but ether has a >>similar dielectric constant. >>Precisely I don't know where to find the following properties: >>* the solvent radius >>* the thermal expansion coefficient >>* the thermal coefficient of the surface tenstion >>* the cavity microscopic coefficient >>* solvent numeral density >>* distances between the first atoms of each type and the cavity (can >>this be just a guess or should this be calculated? And how?) >> >>I have the feeling that usually only water is used as a solvent and that >>although the method in GAMESS is general, the solvent parameters for >>other solvents are not trivial and,thus, other solvents are rarely used. >>Has anybody experience with that? >>Thanks for your attention, >>Ramon Crehuet> >> >> >> >> >> >> >> > > > > From owner-chemistry@ccl.net Fri May 19 10:33:00 2006 From: "Veer Shanmugasundaram Veerabahu.Shanmugasundaram]=[pfizer.com" To: CCL Subject: CCL: Conformational Changes - Animation Message-Id: <-31792-060519103039-24530-UBYGUH3eSeYoR1xe8OMhUQ###server.ccl.net> X-Original-From: "Veer Shanmugasundaram" Date: Fri, 19 May 2006 10:30:37 -0400 Sent to CCL by: "Veer Shanmugasundaram" [Veerabahu.Shanmugasundaram()pfizer.com] Dear CCL'ers: What are some nice tools that you have used to take multiple conformational states of say a protein structure/model and show conformational changes between these states as an animated movie in a presentation. Thanks in advance, Veer ---- Veer Shanmugasundaram, Ph.D Computer-Assisted Drug Discovery, Pfizer Global Research & Development, 2800 Plymouth Road, Ann Arbor, MI 48105. Tel:(734)622-7131 Fax:(734)622-2782 Email:Veerabahu.Shanmugasundaram^pfizer.com From owner-chemistry@ccl.net Fri May 19 11:08:01 2006 From: "Joe Harrison harrison::fermi.phy.uab.edu" To: CCL Subject: CCL: TheRate kinetics code Message-Id: <-31793-060518165531-1067-K03XzD2/GkJ5H38QI/cy0g|-|server.ccl.net> X-Original-From: Joe Harrison Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Thu, 18 May 2006 14:37:12 -0500 (CDT) MIME-Version: 1.0 Sent to CCL by: Joe Harrison [harrison * fermi.phy.uab.edu] I believe it is now part of a CSEO. Check out http://cseo.net Joe Harrison On Thu, 18 May 2006, jim pfaendtner pfaendtner++northwestern.edu wrote: > Sent to CCL by: "jim pfaendtner" [pfaendtner:-:northwestern.edu] > Hi, > > I am looking for a copy of TheRate, I have found several links online, but the code doesn't seem to be readily available any longer. Could anyone provide me with a copy of this? > > thank you. > > Jim> > > From owner-chemistry@ccl.net Fri May 19 11:58:00 2006 From: "Dwayne Joseph dwayne_joseph^-^hotmail.com" To: CCL Subject: CCL:G: Gaussian IOp's Message-Id: <-31794-060519104206-1310-FODmIU5Hak10QmcKSfHBig|server.ccl.net> X-Original-From: "Dwayne Joseph" Content-Type: text/plain; format=flowed Date: Fri, 19 May 2006 14:41:54 +0000 Mime-Version: 1.0 Sent to CCL by: "Dwayne Joseph" [dwayne_joseph(a)hotmail.com] I am using GAUSSIAN98 to perform a relaxed potential surface is scan. Is there an IOp code that gives molecular coefficients for every step of the relaxed scan? -dwayn joseph
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From owner-chemistry@ccl.net Fri May 19 12:52:00 2006 From: "SANDEEP KUMAR skumar23 ~~ jhem.jhu.edu" To: CCL Subject: CCL: Conformational Changes - Animation Message-Id: <-31795-060519123930-624-D4wf5evuzSHrKN9jYUzeHQ * server.ccl.net> X-Original-From: SANDEEP KUMAR Content-Disposition: inline Content-Language: en Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Fri, 19 May 2006 11:39:17 -0400 MIME-Version: 1.0 Sent to CCL by: SANDEEP KUMAR [skumar23###jhem.jhu.edu] Hello Veer: If you have different frames/pictures/conformations of your protein on a PC with Windows, then you can use Windows Movie Maker to arrange them in any sequence you like and make a movie out of it. Sincerely, Sandeep ------------------------------------------------------------------- Dr. Sandeep Kumar, Associate Research Scientist, Johns Hopkins University Department of Biology, 106 Mudd Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA. Phone: 410-516-8433, Email: kumarsan{}jhu.edu. URL: http://myprofile.cos.com/Kumarsan. or https://jshare.johnshopkins.edu/skumar23/public_html/ ----- Original Message ----- > From: "Veer Shanmugasundaram Veerabahu.Shanmugasundaram]=[pfizer.com" Date: Friday, May 19, 2006 10:41 am Subject: CCL: Conformational Changes - Animation > Sent to CCL by: "Veer Shanmugasundaram" > [Veerabahu.Shanmugasundaram()pfizer.com] > Dear CCL'ers: > > What are some nice tools that you have used to take multiple > conformational states of say a protein structure/model and show > conformational changes between these states as an animated movie in > a presentation. > > Thanks in advance, > Veer > ---- > Veer Shanmugasundaram, Ph.D > Computer-Assisted Drug Discovery, > Pfizer Global Research & Development, > 2800 Plymouth Road, > Ann Arbor, MI 48105. > Tel:(734)622-7131 > Fax:(734)622-2782 > Email:Veerabahu.Shanmugasundaram-x-pfizer.com > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > changethe strange characters on the top line to the {} sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Fri May 19 16:10:00 2006 From: "Sten Nilsson Lill stenil _ chem.gu.se" To: CCL Subject: CCL: Conformational Changes - Animation Message-Id: <-31796-060519133551-26188-sv9uuLmQtSBes8RvkxI0MA##server.ccl.net> X-Original-From: "Sten Nilsson Lill" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 19 May 2006 19:35:41 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: "Sten Nilsson Lill" [stenil]![chem.gu.se] Hi, with VMD I have rendered snapshots of an enzyme along a reaction profile. Then it was simple to add the snapshots together to form a movie using Windows Movie Maker. An alternative might be to generate a morph between two different conformations/states. For example if you have two crystal structures which differ in some domain movement you can generate a morph to visualize the movement. I used the web-based tool at http://www.molmovdb.org/ which works really great. Hope this helps, Sten > Sent to CCL by: "Veer Shanmugasundaram" > [Veerabahu.Shanmugasundaram()pfizer.com] > > Dear CCL'ers: > > What are some nice tools that you have used to take multiple > conformational states of say a protein structure/model and show > conformational changes between these states as an animated movie in a > presentation. > > Thanks in advance, > Veer > ---- > Veer Shanmugasundaram, Ph.D > Computer-Assisted Drug Discovery, > Pfizer Global Research & Development, > 2800 Plymouth Road, > Ann Arbor, MI 48105. > Tel:(734)622-7131 > Fax:(734)622-2782 > Email:Veerabahu.Shanmugasundaram-x-pfizer.com> > > > Ph. D. Sten Nilsson Lill Dep. of Chemistry Göteborg University Kemigården 4 S-412 96 Göteborg, Sweden Phone: +46-31-772 2901 Fax: +46-31-772 3840 E-mail: stenil a chem.gu.se Alternative e-mail: slill1 a lsu.edu From owner-chemistry@ccl.net Fri May 19 16:44:01 2006 From: "Elaine Meng meng~!~cgl.ucsf.edu" To: CCL Subject: CCL: Conformational Changes - Animation (Modified by Elaine Meng) Message-Id: <-31797-060519162043-7032-IJRXE1P+Q+C32yQYbRPDYA*server.ccl.net> X-Original-From: Elaine Meng Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Fri, 19 May 2006 12:10:33 -0700 Mime-Version: 1.0 (Apple Message framework v624) Sent to CCL by: Elaine Meng [meng[#]cgl.ucsf.edu] Hi Veer, I'm guessing you don't already have all the intermediate conformations between the states. In this case, the Yale Morph Server may be what you want: http://molmovdb.org/morph/ (Veer: there was a typo in this URL in the first message I sent, sorry!) Good luck, Elaine ----- Elaine C. Meng, Ph.D. meng:cgl.ucsf.edu UCSF Computer Graphics Lab and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco http://www.cgl.ucsf.edu/home/meng/index.html On May 19, 2006, at 7:45 AM, Veer Shanmugasundaram Veerabahu.Shanmugasundaram]=[pfizer.com wrote: > Sent to CCL by: "Veer Shanmugasundaram" > [Veerabahu.Shanmugasundaram()pfizer.com] > > Dear CCL'ers: > > What are some nice tools that you have used to take multiple > conformational states of say a protein structure/model and show > conformational changes between these states as an animated movie in a > presentation. > > Thanks in advance, > Veer > ---- > Veer Shanmugasundaram, Ph.D > Computer-Assisted Drug Discovery, > Pfizer Global Research & Development, > 2800 Plymouth Road, > Ann Arbor, MI 48105. > Tel:(734)622-7131 > Fax:(734)622-2782 > Email:Veerabahu.Shanmugasundaram-x-pfizer.com >