From owner-chemistry@ccl.net Wed Jun 27 00:02:01 2007 From: "Scott Brozell srb/a\osc.edu" To: CCL Subject: CCL: Dock Message-Id: <-34583-070626182802-14127-vVnbMertR7Wom+XGkuQ5TA-x-server.ccl.net> X-Original-From: Scott Brozell Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Tue, 26 Jun 2007 17:26:12 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Scott Brozell [srb]![osc.edu] Hi, On Mon, 25 Jun 2007, Grace Shen sll513,yahoo.com wrote: > I am looking for some references which can give me some instructions or rules on how to do dock manually without using any commercial docking software, such as Glide, Gold, and etc. Your help is highly appreciated! > The DOCK package from UCSF is free to academic researchers. http://dock.compbio.ucsf.edu/ The tutorials and manual at the web site may be helpful for non-DOCK specific docking. Scott From owner-chemistry@ccl.net Wed Jun 27 00:39:00 2007 From: "Rajarshi Guha rguha=-=indiana.edu" To: CCL Subject: CCL: looking for free software to generate descriptors Message-Id: <-34584-070626213559-29031-9ZtgIFAhCKB7QCadvm88KQ^server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Tue, 26 Jun 2007 20:53:45 -0400 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Rajarshi Guha [rguha!^!indiana.edu] On Jun 26, 2007, at 7:22 PM, Grace Shen sll513_._yahoo.com wrote: > Dear All: > > Thank you all very much for the help regarding the "DOCK" question > previously. Now I am wondering if anyone knows there is any free > software which can help me to generate the regular common 1D, 2D > and 3D descriptors so that I can perform QSAR analysis efficiently? > Thanks, CDKDescUI will calculate a number of descriptors - more are being added http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkdesc.html ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Q: What do you get when you cross a Post Modernist with a Mafioso? A: An offer you can't understand. From owner-chemistry@ccl.net Wed Jun 27 02:42:00 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas__chem.elte.hu" To: CCL Subject: CCL: G03 optimization convergence limits Message-Id: <-34585-070626025334-6484-uF/iNo5GcWLCce+QB+dQNQ:server.ccl.net> X-Original-From: =?ISO-8859-1?Q?=D6d=F6n?= Farkas Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Tue, 26 Jun 2007 08:46:33 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas-*-chem.elte.hu] Hi John, I do not advise playing with optimization criteria, even though I used to meet the same kind of problem. Try using GDIIS which usually shows better convergence on flat potential energy surfaces and tight optimization criteria. Also, the following procedure might improve convergence: - Optimize the structure at a lower level using redundant internals (for MM or semiempiricals use Opt=Small) - Start the optimization from the original input geometry using the desired level and read the force constants from the checkpoint file using Opt=ReadFC. The lower level optimization gives a Hessian with good curvature and expected to accelerate the convergence of the real calculation. Best wishes, Ödön On Mon, 2007-06-25 at 13:35 -0400, John McKelvey jmmckel[A]gmail.com wrote: > Greetings, > > Often when there are freely rotating methyl groups one can find that > the energy and gradients have converged but there is a large > displacement because of the freely rotating or librating methyl group, > and a lot of cpu time can go into getting the methyl group to settle > down. Does anyone know how to set IOP info to allow a way around this > problem [where convergence of the torsion angle of the methyl group is > not important]? > > Thanks! > > John McKelvey -- Ödön Farkas Associate professor Deparment of Organic Chemistry and Laboratory of Chemical Informatics, Institute of Chemistry, Eötvös Loránd University, Budapest Address: 1/A Pázmány Péter sétány, H-1117 Budapest, Hungary Phone: +36-1-372-2570 Cell phone: +36-30-255-3111 Fax: +36-1-372-2620 URL: http://organ.elte.hu/farkas From owner-chemistry@ccl.net Wed Jun 27 04:38:01 2007 From: "Roger Kevin Robinson r.robinson#%#imperial.ac.uk" To: CCL Subject: CCL: looking for free software to generate descriptors Message-Id: <-34586-070627043447-4736-kqkLE4hJP9LyI48kxPU80w__server.ccl.net> X-Original-From: Roger Kevin Robinson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 27 Jun 2007 09:32:47 +0100 MIME-Version: 1.0 Sent to CCL by: Roger Kevin Robinson [r.robinson**imperial.ac.uk] Dragon used to be free im not too sure if it is any more there probably a demo. http://www.talete.mi.it/main_net.htm > > Sent to CCL by: Rajarshi Guha [rguha!^!indiana.edu] > > On Jun 26, 2007, at 7:22 PM, Grace Shen sll513_._yahoo.com wrote: > >> Dear All: >> >> Thank you all very much for the help regarding the "DOCK" question >> previously. Now I am wondering if anyone knows there is any free >> software which can help me to generate the regular common 1D, 2D and >> 3D descriptors so that I can perform QSAR analysis efficiently? Thanks, > > CDKDescUI will calculate a number of descriptors - more are being added > > http://cheminfo.informatics.indiana.edu/~rguha/code/java/cdkdesc.html > > > ------------------------------------------------------------------- > Rajarshi Guha > GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE > ------------------------------------------------------------------- > Q: What do you get when you cross a Post Modernist with a Mafioso? > A: An offer you can't understand.http://www.ccl.net/chemistry/sub_unsub.shtml> > Job: http://www.ccl.net/jobsConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Dr. R.Robinson Research Associate Department of Mechanical Engineering Imperial College London - South Kensington Campus London SW7 2AZ UK Tel: +44 20 7589 5111 Ext.57112 Email: r.robinson#%#imperial.ac.uk ABSOLUTISM, OBSOLETISM -- IF IT WORKS, IT'S OUT OF DATE From owner-chemistry@ccl.net Wed Jun 27 05:42:01 2007 From: "Alex A. Granovsky gran a classic.chem.msu.su" To: CCL Subject: CCL: PC GAMESS v. 7.1 final RC is available for beta testers Message-Id: <-34587-070627040104-1058-dM9ws74t6jBB00yOO4sZrQ||server.ccl.net> X-Original-From: "Alex A. Granovsky" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 27 Jun 2007 12:15:53 +0400 MIME-Version: 1.0 Sent to CCL by: "Alex A. Granovsky" [gran#classic.chem.msu.su] Dear GAMESS users! After more than year of constant development, we are glad to announce the start of the PC GAMESS v. 7.1 beta test program. The new PC GAMESS version incorporates changes introduced since the original PC GAMESS version 7.0 became available, which are documented in the "History" and "News" sections of the PC GAMESS homepage at MSU. It also features the completely new state-of-the-art semidirect parallel MP2 gradient program with low memory demands, excellent scalability and performance. The beta test program is open for all registered PC GAMESS users. Please send your requests back to us and we'll provide you by the information on how to download the PC GAMESS v. 7.1 final RC binaries. Best regards, Alex Granovsky From owner-chemistry@ccl.net Wed Jun 27 09:40:01 2007 From: "bala bala(~)igib.res.in" To: CCL Subject: CCL: information on books ... Message-Id: <-34588-070627092556-22089-S5C7zrNjV0bzhM9dwgPLXQ(!)server.ccl.net> X-Original-From: "bala" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C7B8B8.E6BFDE7D" Date: Wed, 27 Jun 2007 18:14:28 +0530 MIME-Version: 1.0 Sent to CCL by: "bala" [bala%%igib.res.in] This is a multi-part message in MIME format. ------_=_NextPart_001_01C7B8B8.E6BFDE7D Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hello, I am looking for some books on spectroscopic techniques. I want one = which is devoted especially in application of spec. tech in nucleic acid = sciences. Can anyone please suggest me some.=20 Thank you in advance, Balasubramanian. ------_=_NextPart_001_01C7B8B8.E6BFDE7D Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable information on books

Hello,

I am looking for some books on spectroscopic techniques. I want one = which is devoted especially in application of spec. tech in nucleic acid = sciences. Can anyone please suggest me some.

Thank you in advance,
Balasubramanian.

------_=_NextPart_001_01C7B8B8.E6BFDE7D-- From owner-chemistry@ccl.net Wed Jun 27 10:52:00 2007 From: "navizet(a)univ-mlv.fr navizet(a)univ-mlv.fr" To: CCL Subject: CCL:G: amber force field specification for dihedral in Gaussian input Message-Id: <-34589-070627051710-23178-+rc/yWU3uw3hOZ/q5Aqd9Q*server.ccl.net> X-Original-From: "navizet[*]univ-mlv.fr" Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=iso-8859-1 Date: Wed, 27 Jun 2007 04:02:44 -0400 MIME-Version: 1.0 Sent to CCL by: "navizet-*-univ-mlv.fr" [navizet-*-univ-mlv.fr] Hi CCLers, I would like to manually specify amber dihedral torsion in a gaussian input in order to do ONIOM calculation. In the Gaussian Manual, one can read : Amber torsion (Amber [1]): Σi=1,4 (Magi*[1+cos(i*θ-I(i+4))])/NPaths AmbTrs Atom-type1 A-type2 A-type3 A-type4 PO1 PO2 PO3 PO4 Mag1 Mag2 Mag3 Mag4 NPaths PO1-PO4 Phase offsets Mag1...Mag4 V/2 magnitudes NPaths Number of paths (if < 0, determined on-the-fly). I have some questions about the equation : where does it come from ? What is the I(i+4) ? I gess it is the POi ? I also do not understand why there is 4 phase offsets, 4 V/2 When looking the Amber force field, torsion need periodicity : how Gaussian know the periodicity then ? I would say that if the period is 4 (for example) then I feel the PO4 and Mag4 data and put zero for the other. Am I right ? I would really like to know what I am doing (and not just guess) so if you have already experience with this, help me. Thank you in advance. Isabelle -------------------------------------------------------------------- mail2web.com – Enhanced email for the mobile individual based on Microsoft® Exchange - http://link.mail2web.com/Personal/EnhancedEmail From owner-chemistry@ccl.net Wed Jun 27 12:06:01 2007 From: "Ivanciuc, Ovidiu I. oiivanci|a|utmb.edu" To: CCL Subject: CCL: looking for free software to generate descriptors Message-Id: <-34590-070627115835-22251-Oa3FgK2BgJramveFTF6Efw]=[server.ccl.net> X-Original-From: "Ivanciuc, Ovidiu I." Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Wed, 27 Jun 2007 09:54:12 -0500 MIME-Version: 1.0 Sent to CCL by: "Ivanciuc, Ovidiu I." [oiivanci]*[utmb.edu] >>> Dragon used to be free im not too sure if it is any more there probably A fully functional and free version of Dragon is available on-line from the Virtual Computational Chemistry Laboratory, http://www.vcclab.org/ E-DRAGON computes 1600 descriptors for a maximum of 149 molecules in a batch, http://www.vcclab.org/lab/edragon/ QSAR applications of DRAGON descriptors may be found in the Internet Electronic Journal of Molecular Design (IEJMD), http://www.biochempress.com Try also Parameter Client (PCLIENT) which incorporates E-DRAGON and computes more than 3000 descriptors http://www.vcclab.org/lab/pclient/ For docking, AutoDock http://autodock.scripps.edu/ is free and it is the most cited docking software (27% compared with 6% for Dock, see http://autodock.scripps.edu/news_files/autodock-is-the-most-cited-docking-software). A Windows version of AutoDock is available (requires cygwin), and it is very fast. Regards, Ovidiu ###################################### Ovidiu Ivanciuc Sealy Center for Structural Biology and Molecular Biophysics Department of Biochemistry and Molecular Biology University of Texas Medical Branch 301 University Boulevard Galveston, Texas 77555-0857 USA URL: http://ivanciuc.org/ Email: iejmd!=!yahoo.com IEJMD: http://www.biochempress.com