From owner-chemistry@ccl.net Mon Apr 14 08:43:01 2008 From: "Lingyun Wang james_0217[*]hotmail.com" To: CCL Subject: CCL: Asking for help of Binding Energy by Amber Message-Id: <-36721-080413004158-5339-td4/YbMf2/5NDjTMCsIafg _ server.ccl.net> X-Original-From: "Lingyun Wang" Date: Sun, 13 Apr 2008 00:41:55 -0400 Sent to CCL by: "Lingyun Wang" [james_0217.%.hotmail.com] Sent to CCL by: "Lingyun Wang" [james_0217%hotmail.com] Dear colleagues, I have a question about how can I use Amber software to calculate the Binding Energy in explict model. Is MM-PBSA is only for implict model? Thank you! Lingyun Wang From owner-chemistry@ccl.net Mon Apr 14 10:36:01 2008 From: "Metwally, Essam emetwall*_*tripos.com" To: CCL Subject: CCL: display probleme when executing a sybyl spl script Message-Id: <-36722-080414103422-7927-Z++kACqIuFv0PqdvZsMcig(!)server.ccl.net> X-Original-From: "Metwally, Essam" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 14 Apr 2008 09:33:50 -0500 MIME-Version: 1.0 Sent to CCL by: "Metwally, Essam" [emetwall,,tripos.com] Dear M.Meslamani, Your issue is the mixture of shell script with an SPL script. When you start the shell script it will expand all variables, ie all "$var_name" strings to their values in the shell. If you need to mix the two formats then any variables known only to SYBYL must be escaped, so: $search_nrbonds --> \$search_nrbonds That should correct your issues. -- Essam ---------------------------- Dr Essam Metwally Senior Development Scientist Tripos International emetwall++tripos.com Tel +314 951 3260 ---------------------------- Announcing SYBYL 8.0 - with a fresh new look and feel. Install it today - you'll be glad you did! jamel-eddine.meslamani*_*ulp.u-strasbg.fr wrote: > > Sent to CCL by: jamel-eddine.meslamani _ ulp.u-strasbg.fr > Dear members, > > I have some variable's display problem when I execute an spl script, I > got this as a result if I'd like to echo a variable: > > in the script: > echo $sybyl_version > echo $search_nrbonds > > terminal result after executing the script: > SYBYL> ECHO > > SYBYL> ECHO > > After performing the systematic search,even if I try to use the > variable, it seems to be misssing.The $sybyl_version is also undisplayed. > Does anyone has an idea? > Thank you in advance. > > MESLAMANI Jamelhttp://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Mon Apr 14 11:43:00 2008 From: "Anouar Benali Anouar.Benali::ensiacet.fr" To: CCL Subject: CCL: VASP calculation Message-Id: <-36723-080414113915-4417-SjXKadwOWugm3TVqtdhirQ#server.ccl.net> X-Original-From: Anouar Benali Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 14 Apr 2008 17:07:39 +0200 MIME-Version: 1.0 Sent to CCL by: Anouar Benali [Anouar.Benali*ensiacet.fr] Hi I don't know if many of you use the Vienna Ab-initio Simulation Package (VASP) but i tried to work on the charges calculations by increasing or decreasing the Wigner-Sietz radius. I tried to encrease or decrease the RWIGS parameter onthe INCAR file, but somehow no matter what value I choose, nothing happens on the charges calculations. The RWIGS parameter is supposed to be the Wigner Sitez radius, so by decreasing it I should have taken less electrons in account. but even by entering an non coherent value nothing changes at all. I can see on the OUTCAR file that it has been taking in account, so vasp chooses the one i entered but it doesn't change a thing. The main problem comes from the fact that while studiying Aluminum, the charges calculations give only 0.8 electron instead of the 3 valence electrons on Al. Is there something i did wrong? Thank you very much Anouar Benali Ph. D student/^ //CIRIMAT, ENSIACET UMR CNRS 5085 118 route de Narbonne, 31077 Toulouse cedex 4/ From owner-chemistry@ccl.net Mon Apr 14 13:46:01 2008 From: "David A. Case case__scripps.edu" To: CCL Subject: CCL: Asking for help of Binding Energy by Amber Message-Id: <-36724-080414115607-11781-fQHTY0kxPjhhzYV5YFtj+g!A!server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 14 Apr 2008 08:55:28 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case*|*scripps.edu] On Sun, Apr 13, 2008, Lingyun Wang james_0217[*]hotmail.com wrote: > > I have a question about how can I use Amber software to calculate the > Binding Energy in explict model. Is MM-PBSA is only for implict model? Yes: MM-pbsa is only for use with implicit solvation models. You can use thermodynamic integration or umbrella sampling to compute absolute or relative binding free energies in explicit solvent. See Sections 6.5-6.7 of the Users' Manual. You may want to consider Amber10, which has improved capabilities in this area. Also, it is generally better to post Amber-related questions to its mailing list. See http://ambermd.org for more information. ...good luck...dave case From owner-chemistry@ccl.net Mon Apr 14 14:20:01 2008 From: "David A. Case case{:}scripps.edu" To: CCL Subject: CCL: ANNOUNCEMENT: release of Amber 10 Message-Id: <-36725-080414131914-6507-NwXtTS/cWcuCtGjinEy0/g*server.ccl.net> X-Original-From: "David A. Case" Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 14 Apr 2008 10:18:40 -0700 Mime-Version: 1.0 Sent to CCL by: "David A. Case" [case,+,scripps.edu] I am pleased to announce the release Amber 10. Amber is a suite of programs designed for molecular dynamics simulations of biomolecules. For full information on what is new in Amber 10, and how to order it, please see: http://ambermd.org ...dave case (For the Amber development team: http://ambermd.org/contributors.html ) From owner-chemistry@ccl.net Mon Apr 14 20:19:00 2008 From: "Alexander Hoepker achoepker!A!gmail.com" To: CCL Subject: CCL:G: parallel processing in Gaussian Message-Id: <-36726-080414172759-8534-fiEbAZGe9n//KFifYUHeUg[A]server.ccl.net> X-Original-From: "Alexander Hoepker" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 14 Apr 2008 15:48:17 -0400 MIME-Version: 1.0 Sent to CCL by: "Alexander Hoepker" [achoepker%x%gmail.com] I'm a running Gaussian 03 calculations on a dual quad core xeon machine (Linux) with a total of 16 GB and would like to take advantage of all eight cores. I used the %NProcShared=8 command and this appeared to work just fine. However, the number of shared processors keeps getting reduced. CouldSu: requested number of processors reduced to : 2 ShMem 1 Linda Should the number of processors shared be 2 instead and would it take advantage of all eight cores? Also, why does it mention Linda if I'm not trying to parallel process with separate machines? Thanks for your help in advance Alex From owner-chemistry@ccl.net Mon Apr 14 21:38:00 2008 From: "gnli gnli*dicp.ac.cn" To: CCL Subject: CCL: theory relate to circular dichroism sepctrum (ECD) Message-Id: <-36727-080414204928-5491-NQrXYbYpA99BcMtNbUF9Vg.@.server.ccl.net> X-Original-From: "gnli" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-2022-jp" Date: Tue, 15 Apr 2008 08:48:23 +0800 MIME-Version: 1.0 Sent to CCL by: "gnli" [gnli*dicp.ac.cn] Dear CCLer, I got my first seminar title : theory and experiment of circular dichroism spectrum (CD)$B!$(BI download some articles but most of them is about experimental and dft calculate result. they are hardly refer to the basic theory of CD in the introduction or theory part. I will very appreciate if anyone can recommend some paper about the theory of CD for me. Thank you ! best wishes Guanna Li gnli(~)dicp.ac.cn From owner-chemistry@ccl.net Mon Apr 14 23:52:00 2008 From: "zhendong zhao zzhao(_)olemiss.edu" To: CCL Subject: CCL: theory relate to circular dichroism sepctrum (ECD) Message-Id: <-36728-080414231633-7821-6HI1k07vMNp7Ix5iu0+55Q . server.ccl.net> X-Original-From: zhendong zhao Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=GB2312 Date: Mon, 14 Apr 2008 22:12:11 -0500 Mime-Version: 1.0 Sent to CCL by: zhendong zhao [zzhao^olemiss.edu] Hi, Maybe you can refer the paper. "The Ab Initio Calculation of Molecular Chiroptical Properties," T.D. Crawford, Theor. Chem. Acc. 115, 227-245 (2006). On Tue, 15 Apr 2008 08:48:23 +0800 "gnli gnli*dicp.ac.cn" wrote: > > Sent to CCL by: "gnli" [gnli*dicp.ac.cn] > Dear CCLer, > I got my first seminar title : theory and experiment of circular > dichroism spectrum (CD)£¬I download some articles but most of them is > about experimental and dft calculate result. > they are hardly refer to the basic theory of CD in the introduction or > theory part. > I will very appreciate if anyone can recommend some paper about the > theory of CD for me. > Thank you ! > > best wishes > Guanna Li > gnli..dicp.ac.cn > > > > -= 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 -,- sign. You can > also> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> >