From owner-chemistry@ccl.net Thu Sep 4 04:57:01 2008 From: "Brian Salter-Duke brian.james.duke|gmail.com" To: CCL Subject: CCL:G: Online course in computational chemistry Message-Id: <-37708-080904033639-32143-2I38GdkHabJumuhrOs1j7A]~[server.ccl.net> X-Original-From: Brian Salter-Duke Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 04 Sep 2008 16:48:09 +1000 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke(!)gmail.com] naser eltaher Eltayeb nasertaha90~!~yahoo.co.uk wrote: > Sent to CCL by: "naser eltaher Eltayeb" [nasertaha90/./yahoo.co.uk] > Hi All > > Is there any institute of University offer online or distance learning course in computational chemistry? > > Naser Eltaher Eltayeb Let me first indicate that the ACCVIP online course has NOT been offered since 2001. Some details are still at: http://www.salter-duke.bigpondhosting.com/brian/msc/index.html In spite of that, I still get several inquiries a year. This is sad, but we never got many students actually enrolling and we can no longer run it. I am trying to get these materials uploaded to wikiversity, but there are several problems:- 1) I am finding it difficult to find the time. 2) The Jmol wiki extension does not run on wikimedia projects, such as wikipedia and wikiversity. 3) I need to write a lot of scripts to replace use of non-free programs such as Gaussian by free programs. Nevertheless this is an exciting project, at least to me, and if it could be implemented and expanded it could be very useful. We could perhaps develop a free community to help students with the material, although it would not lead to a degree. If anyone is interested, please e-mail, although if you are going to WATOV, please wait and talk to me there. Brian. -- Brian Salter-Duke (Brian Duke) Brian.James.Duke]~[gmail.com Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia http://www.salter-duke.bigpondhosting.com/brian/index.htm Honorary Researcher Fellow, Monash Institute of Pharmaceutical Sciences From owner-chemistry@ccl.net Thu Sep 4 07:56:01 2008 From: "Vivek sharma vivek.viv.sharma,+,gmail.com" To: CCL Subject: CCL: QC programs Message-Id: <-37709-080904075311-22687-hVqZWFGbr8sJfcYqtJ6j+w..server.ccl.net> X-Original-From: "Vivek sharma" Date: Thu, 4 Sep 2008 07:53:08 -0400 Sent to CCL by: "Vivek sharma" [vivek.viv.sharma.:.gmail.com] Dear CCL people, I am new to Quantum Chemistry field. I have started to use semi-empirical calculations on small molecules (ligand molecules) to obtain partial charges mainly. For this purpose I have been using MOPAC in GHEMICAL. Now, I am proceeding to high level ab-initio calculations and I would like to gather some information about the software packages available. I would like to install the ab initio QC calculations package on a larger machine (linux cluster) and would like to make it run in parallel over the compute nodes. Would you please suggest some good QC packages, which are free and not so difficult to parallelise and install (?) and can be run over remote machine too. I have got some feedbacks about NWChem and Gamess. Would you also please throw some light on these two packages (?). Sorry if it sounds vague, but I think all inputs will be very valuable. thanks in advance, Vivek -- VIVEK SHARMA IMM, India. From owner-chemistry@ccl.net Thu Sep 4 12:59:01 2008 From: "amine amine m-22]^[hotmail.fr" To: CCL Subject: CCL: ATTN, need revision Message-Id: <-37710-080904125718-23591-hTitDK8LdE2528rtmp+xtg .. server.ccl.net> X-Original-From: "amine amine" Date: Thu, 4 Sep 2008 12:57:14 -0400 Sent to CCL by: "amine amine" [m-22(~)hotmail.fr] Hi I have amber10 and when i run 1/ antechamber -fi pdb -fo prepi -i input.pdb -o output.prepi -c bcc -at gaff -j 4 2/ parmchk -i tp.prepin -o tp.frcmod -f prepi -p gaff_parm99m.dat this is my frcmod file ANGLE oh-c3-h1 0.000 0.000 ATTN, need revision oh-c3-c3 0.000 0.000 ATTN, need revision ho-oh-c3 0.000 0.000 ATTN, need revision c3-c3-os 0.000 0.000 ATTN, need revision c3-c3-h1 0.000 0.000 ATTN, need revision c3-c3-c3 0.000 0.000 ATTN, need revision h1-c3-h1 0.000 0.000 ATTN, need revision c3-os-c3 0.000 0.000 ATTN, need revision os-c3-h1 0.000 0.000 ATTN, need revision os-c3-h2 0.000 0.000 ATTN, need revision os-c3-os 0.000 0.000 ATTN, need revision c3-c3-h2 0.000 0.000 ATTN, need revision DIHE oh-c3-c3-os 1 0.000 0.000 0.000 ATTN, need revision oh-c3-c3-h1 1 0.000 0.000 0.000 ATTN, need revision oh-c3-c3-c3 1 0.000 0.000 0.000 ATTN, need revision ho-oh-c3-h1 1 0.000 0.000 0.000 ATTN, need revision ho-oh-c3-c3 1 0.000 0.000 0.000 ATTN, need revision c3-c3-os-c3 1 0.000 0.000 0.000 ATTN, need revision c3-c3-c3-os 1 0.000 0.000 0.000 ATTN, need revision c3-c3-c3-h1 1 0.000 0.000 0.000 ATTN, need revision c3-c3-c3-c3 1 0.000 0.000 0.000 ATTN, need revision h1-c3-c3-os 1 0.000 0.000 0.000 ATTN, need revision h1-c3-c3-h1 1 0.000 0.000 0.000 ATTN, need revision c3-os-c3-h2 1 0.000 0.000 0.000 ATTN, need revision c3-os-c3-os 1 0.000 0.000 0.000 ATTN, need revision os-c3-c3-os 1 0.000 0.000 0.000 ATTN, need revision h1-c3-os-c3 1 0.000 0.000 0.000 ATTN, need revision c3-c3-c3-h2 1 0.000 0.000 0.000 ATTN, need revision oh-c3-c3-oh 1 0.000 0.000 0.000 ATTN, need revision oh-c3-c3-h2 1 0.000 0.000 0.000 ATTN, need revision h1-c3-c3-h2 1 0.000 0.000 0.000 ATTN, need revision IMPROPER NONBON oh 0.0000 0.0000 ATTN, need revision ho 0.0000 0.0000 ATTN, need revision c3 0.0000 0.0000 ATTN, need revision h1 0.0000 0.0000 ATTN, need revision os 0.0000 0.0000 ATTN, need revision h2 0.0000 0.0000 ATTN, need revisio what's wrong?? From owner-chemistry@ccl.net Thu Sep 4 15:43:00 2008 From: "Barry Hardy barry.hardy-#-vtxmail.ch" To: CCL Subject: CCL: eCheminfo Drug Discovery Informatics 2008 Program and Abstracts (Bryn Mawr) Message-Id: <-37711-080904151806-14085-8+TsXXAxM91YzPNeHCEPXQ*o*server.ccl.net> X-Original-From: Barry Hardy Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 04 Sep 2008 20:17:39 +0200 MIME-Version: 1.0 Sent to CCL by: Barry Hardy [barry.hardy .. vtxmail.ch] I have posted the full set of abstracts for the eCheminfo Community of Practice Meeting taking place at Bryn Mawr College 14-17 October 2008 at the addresses below. Relevant feedback, comments, discussion, new developments etc. welcome as comments in the blog areas prior to the meeting discussions. Docking & Scoring http://barryhardy.blogs.com/cheminfostream/2008/09/docking-and-sco.html Free Energy Methods in Drug Discovery http://barryhardy.blogs.com/cheminfostream/2008/08/free-energy-met.html In Silico Chemogenomics http://barryhardy.blogs.com/cheminfostream/2008/09/in-silico-chemo.html Accurate Calculation of pKas http://barryhardy.blogs.com/cheminfostream/2008/08/accurate-calcul.html Computational Biology http://barryhardy.blogs.com/cheminfostream/2008/08/computational-b.html PDB Ligands; Analysing their Structure and Binding Data http://barryhardy.blogs.com/cheminfostream/2008/08/pdb-ligands-ana.html Predictive ADME http://barryhardy.blogs.com/cheminfostream/2008/08/predictive-adme.html Predictive Toxicology http://barryhardy.blogs.com/cheminfostream/2008/08/computer-based.html best regards Barry Hardy PhD eCheminfo Community of Practice & Research Douglas Connect, Switzerland Tel: +41 61 851 0170 Email: Barry.Hardy -(at)- douglasconnect (dot) com From owner-chemistry@ccl.net Thu Sep 4 16:45:00 2008 From: "Marcelo Puiatti marcelo.puiatti=gmail.com" To: CCL Subject: CCL: Processor differencies Message-Id: <-37712-080904163041-4096-71ka0UC3iFOIbTJDpLj1Zw- -server.ccl.net> X-Original-From: "Marcelo Puiatti" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 4 Sep 2008 15:37:52 -0300 MIME-Version: 1.0 Sent to CCL by: "Marcelo Puiatti" [marcelo.puiatti~~gmail.com] Hi: I am a chemist trying to configure a machine, and I have a question about processor specification. I am interested in the a Xeon Quad core X-5472 3.00 GHz, or similar, which is the AMD processor with similar characteritics or performance? AMD opteron, or AMD Barcelona? Thanks in advance Marcelo Puiatti From owner-chemistry@ccl.net Thu Sep 4 23:57:01 2008 From: "Antonio De Crisci antonio.decrisci{}utoronto.ca" To: CCL Subject: CCL: positive and negative virtual orbital energies Message-Id: <-37713-080904235546-2839-TAKQx5GY6Ky8UGkokACC/A/./server.ccl.net> X-Original-From: "Antonio De Crisci" Date: Thu, 4 Sep 2008 23:55:43 -0400 Sent to CCL by: "Antonio De Crisci" [antonio.decrisci..utoronto.ca] Hello All, Is there a given rule for how many virtual orbitals can have negative energies before it becomes positive? Do the rules change for restricted Vs. unrestricted calculations? Some of my calculations have up to 30 negative virtual orbitals that have negative energies. However, some of my caculations only have 3 negative virtual orbitals before they start going positive. I just want to know what this means. Thanks, Anthony