From owner-chemistry@ccl.net Sun Mar 8 03:05:01 2009 From: "Jeff Woodford jwoodfor---eou.edu" To: CCL Subject: CCL: Hartree-Fock library? Message-Id: <-38794-090308030328-6824-d3jRwebDKMPwr3DYJMgDWQ..server.ccl.net> X-Original-From: "Jeff Woodford" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Sun, 8 Mar 2009 01:03:27 -0600 MIME-Version: 1.0 Sent to CCL by: "Jeff Woodford" [jwoodfor/./eou.edu] Greetings: Is there such a thing as a computational library or API that would perform a simple Hartree-Fock calculation, that could be called from within a Fortran/C program? I'm thinking something analogous to the BLAS/LAPACK library of linear algebra routines. Thanks, -Jeff Jeffrey N. Woodford Associate Professor of Chemistry Eastern Oregon University Tel: 541-962-3321 Fax: 541-962-3873 From owner-chemistry@ccl.net Sun Mar 8 09:23:01 2009 From: "hirdesh kumar hirdeshs8(0)gmail.com" To: CCL Subject: CCL: Server for rational drug design Message-Id: <-38795-090308092057-19795-yu44WBfbxtIDGY7A/XA3wA=server.ccl.net> X-Original-From: hirdesh kumar Content-Type: multipart/alternative; boundary=0016e652ff9a9f218e04649b62de Date: Sun, 8 Mar 2009 18:50:44 +0530 MIME-Version: 1.0 Sent to CCL by: hirdesh kumar [hirdeshs8[A]gmail.com] --0016e652ff9a9f218e04649b62de Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi All; I want to design novel molecules for protein's cavity. Is there any freely available software or server is available for structure based rational drug design? --0016e652ff9a9f218e04649b62de Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Hi All;
I want to design novel molecules for protein's cavity. Is there any freely available software or server is available for structure based rational drug design?

--0016e652ff9a9f218e04649b62de-- From owner-chemistry@ccl.net Sun Mar 8 12:10:00 2009 From: "Laura Gillman laura++molecular-conceptor.com" To: CCL Subject: CCL: Cheminformatics and Drug Design: New Learning Resource Message-Id: <-38796-090308094148-28742-LTWGvo9v0EpuGEdDzMOg9g||server.ccl.net> X-Original-From: "Laura Gillman" Date: Sun, 8 Mar 2009 09:41:44 -0400 Sent to CCL by: "Laura Gillman" [laura]|[molecular-conceptor.com] The new Molecular Conceptor Learning Series has been released - a new series of computer-based training modules that have been designed to give researchers in the field of drug design, the comprehensive knowledge necessary to succeed in daily virtual drug design tasks. The five modules that make up the Molecular Conceptor Learning Series are: * Drug Design * Cheminformatics * Medicinal Chemistry * Structural Bioinformatics * Practical Drug Discovery: Case Studies For more information visit: http://www.drugdesign.com From owner-chemistry@ccl.net Sun Mar 8 20:00:01 2009 From: "Neha Gandhi n.gandhiau..gmail.com" To: CCL Subject: CCL: MM-PBSA calculation in Gromacs Message-Id: <-38797-090308195821-27552-srS2Vp8m66V5TLMDE2Nu7A*_*server.ccl.net> X-Original-From: Neha Gandhi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Mon, 9 Mar 2009 07:58:09 +0800 MIME-Version: 1.0 Sent to CCL by: Neha Gandhi [n.gandhiau^gmail.com] Hi, Did anyone tried running mm-pbsa using gromacs trajectories? Are there any scripts to run mm-pbsa calculations in gromacs? Kindly help! -- Regards, Neha Gandhi, School of Biomedical Sciences, Curtin University of Technology, GPO Box U1987 Perth, Western Australia 6845 From owner-chemistry@ccl.net Sun Mar 8 21:53:00 2009 From: "Christoph Riplinger cri#%#thch.uni-bonn.de" To: CCL Subject: CCL:G: QM/MM question Message-Id: <-38798-090308122902-6135-jD7o1Y8CvgcWISP6NXIMiw[a]server.ccl.net> X-Original-From: Christoph Riplinger Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Sun, 08 Mar 2009 16:28:38 +0100 Mime-Version: 1.0 Sent to CCL by: Christoph Riplinger [cri_-_thch.uni-bonn.de] Dear Maurizzio, The quantum chemistry package ORCA is free for academic users (http://www.thch.uni-bonn.de/tc/orca/). It is coupled to a series of QMMM softwares: Gromacs, Chemshell, QMMM (Lin, Truhlar) and pDynamo. The experience in our group shows that you can easily do geometry optimizations (minima and TS) and property calculations for protein systems with ORCA/gromacs. Furthermore the ORCA group is currently working together with gromacs to set up a standard QM/MM-workflow for protein systems containing non-standard residues. Best regards, Christoph Am Freitag, den 06.03.2009, 01:08 -0500 schrieb Maurizzio m.argonni[]gmail.com: > Dear CCL'ers: > > I would like to perform some QM/MM calculations but I don't seem to be > able to find adequate software for it that is free for academic use. > Are the choices really so limited? So far, I am aware of GAMESS > interfaced to a very dated version of Tinker and then QMMM software > from Dr. Truhlar's lab that is able to use also GAMESS and Tinker > albeit in a limited way because of limitations in GAMESS. > > I have no money to pay for Gaussian or Schrodinger's Qsite and I sort > of refuse to pay 500 UK Pounds for Chemshell on the basis that I am > not British (not to mention that most of the software they use as a > base for theirs is free and/or developed elsewhere). > > Anyway, I would appreciate any insights into what choices I have for > QM/MM software that would allow me to do calculations like geometry > optimizations, transition states, etc. in protein systems. Thanks for > the help! > > Maurizzio > >