From owner-chemistry@ccl.net Wed Feb 28 04:26:01 2007 From: "Michel Petitjean ptitjean[A]itodys.jussieu.fr" <owner-chemistry:server.ccl.net> To: CCL Subject: CCL: small molecule volume calculation Message-Id: <-33706-070228042013-18970-F9VdfwPh6YcOW7NbzhF3MQ:server.ccl.net> X-Original-From: Michel Petitjean <ptitjean.:.itodys.jussieu.fr> Date: Wed, 28 Feb 2007 10:19:47 +0100 (MET) Sent to CCL by: Michel Petitjean [ptitjean.++.itodys.jussieu.fr] To: chemistry++ccl.net Subject: CCL: Re: small molecule volume calculation If the atomic radii are large (and particularly if they are augmented by 1.4 A), you should have intersections of more than 3 spheres (4,5,6, or 7 intersecting spheres are frequently observed). In this situation, you must use an analytical calculation program indeed handling this situation, as ASV: see my paper in J. Comput. Chem. 1994,15[5],507-523. ASV is downloadable for free: programme and documentation are on http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html#ASV Michel Petitjean, Email: petitjean++itodys.jussieu.fr ITODYS (CNRS, UMR 7086) ptitjean++ccr.jussieu.fr 1 rue Guy de la Brosse Phone: +33 (0)1 44 27 48 57 75005 Paris, France. FAX : +33 (0)1 44 27 68 14 http://petitjeanmichel.free.fr/itoweb.petitjean.spheres.html Sent to CCL by: "Veronica Tello" [vtellof:_:gmail.com] > Greetings. > I have calculated the volume of some cavities on a protein using the on-line program CASTp (keeping the 1.4 probe radius). I wish to calculate the volume of some possible ligands and compare results. > I have access to HyperChem7. Using it, I get very different volume values when choosing either Van der Waals surface or Sovent-Accesible Surface. > Which option is better suited in this case? Can someone recomend a different program (preferably open-access)? > Thank you very much. > > Veronica Tello F > Instituto de Quimica, UNAM > vtellof^^gmail.com From owner-chemistry@ccl.net Wed Feb 28 05:01:01 2007 From: "Pradipta Bandyopadhyay pradipta:iitg.ernet.in" <owner-chemistry###server.ccl.net> To: CCL Subject: CCL:G: Question on Gaussian Network Model ! Message-Id: <-33707-070228020001-8809-rNRnCFiiyV7ZwWtS63fJ2Q###server.ccl.net> X-Original-From: "Pradipta Bandyopadhyay" <pradipta(0)iitg.ernet.in> Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 28 Feb 2007 11:37:36 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Pradipta Bandyopadhyay" [pradipta-*-iitg.ernet.in] Dear All, For the experts on Gaussian Network Model (GNM): Applying GNM to a protein (whose structure is a bit open), I found that in some regions B-factors obtained from calculation is different from experimental one (for the rest other regions these are close). This probably means using one gamma may not be enough. Does anyone know if there is any simple way to use more than one gamma in GNM (any other suggestion would be appreciated also)? thanks, Pradipta Dr. Pradipta Bandyopadhyay Assistant Professor Dept. of Biotechnology Indian Institute of Technology, Guwahati web: http://202.141.80.5/~pradipta/Pradipta.htm ----------------------------------------------------------------------------------- This email was sent from IIT Guwahati Webmail. If you are not the intended recipient, please contact the sender by email and delete all copies; your cooperation in this regard is appreciated. http://www.iitg.ernet.in From owner-chemistry@ccl.net Wed Feb 28 05:56:01 2007 From: "Jens Spanget-Larsen spanget\a/ruc.dk" <owner-chemistry*server.ccl.net> To: CCL Subject: CCL:G: frequency output Message-Id: <-33708-070228043902-25248-2hwD1ga3qFVWd/FbNh5DVQ*server.ccl.net> X-Original-From: Jens Spanget-Larsen <spanget[#]ruc.dk> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 28 Feb 2007 10:38:40 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget:_:ruc.dk] Dear Neeraj Misra Misraneeraj, if I understand correctly, the 'Frequency' option 'InternalModes' leads a print of normal modes as displacements in redundant internal coordinates. Hence, a potential energy distribution analysis is not performed, and an energy scaling is irrelevant. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget++ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ neeraj misra misraneeraj]=[gmail.com wrote: > Sent to CCL by: "neeraj misra" [misraneeraj##gmail.com] DO WE HAVE > TO SCALE THE POTENTIAL ENERGY DISTRIBUTIONS GIVEN IN THE FREQUENCY > OUTPUT WHEN WE GIVE FREQ=INTERNAL AS THE ADDITIONAL KEYWORD IN A > FREQUENCY CALCULATION BY GAUSSIAN O3W. I AM ATTACHING THE OUTPUT OF A > FREQ CALCULATION WHICH GIVES THE NORMAL MODES ALSO.PLEASE CLARIFY > THIS DOUBT. THANKS IN ADVANCE From owner-chemistry@ccl.net Wed Feb 28 07:13:00 2007 From: "Tanja van Mourik tanja.vanmourik|a|st-andrews.ac.uk" <owner-chemistry^^^server.ccl.net> To: CCL Subject: CCL:G: EPR on excited states - summary Message-Id: <-33709-070228070648-1921-ZC30RqnCW/yWeEezLTlCMg^^^server.ccl.net> X-Original-From: Tanja van Mourik <tanja.vanmourik-,-st-andrews.ac.uk> Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Wed, 28 Feb 2007 11:36:53 +0000 MIME-Version: 1.0 Sent to CCL by: Tanja van Mourik [tanja.vanmourik * st-andrews.ac.uk] Hi All, Please see below a summary regarding my query on the calculation of EPR parameters in electronically excited molecules. With many thanks to Helen Tsiu, Douglas Fox and Frank Neese. Doug Fox pointed out that these calculations require a one-particle density matrix and that the CIS methods in Gaussian 03 can produce this using # CIS(Root=n)/basis Density Prop=EPR which will request calculation of the CIS density for a selected root n. The Prop=EPR will compute the anisotropy EPR terms. By default only the isotropic terms are produced. Helen Tsui mentioned that, in Gaussian, Freq=(VCD, VibRot[, Anharmonic]) will produce Hyperfine spectra tensors (incl. g tensors). Frank Neese pointed me to the free program Orca (http://www.thch.uni-bonn.de/tc/orca/). Orca has comprehensive EPR capabilities and excited triplet states should present no particular problem. Orca was also recommended by Helen Tsui, who mentioned in addition that ADF can calculate EPR parameters as well. Best wishes, Tanja -- ================================================================= Tanja van Mourik Royal Society University Research Fellow School of Chemistry, University of St. Andrews North Haugh, St. Andrews Fife KY16 9ST, Scotland (UK) email: tanja.vanmourik(~)st-andrews.ac.uk web: http://chemistry.st-and.ac.uk/staffmember.php?id=tvm ================================================================= ------------------------------------------------------------------ University of St Andrews Webmail: https://webmail.st-andrews.ac.uk From owner-chemistry@ccl.net Wed Feb 28 15:17:00 2007 From: "Jeff Nauss jnauss ~~ accelrys.com" <owner-chemistry|server.ccl.net> To: CCL Subject: CCL: Accelrys Customer Training for April Message-Id: <-33710-070228151303-1665-bdq0JDAV4heSV8GMhZU1Bw|server.ccl.net> X-Original-From: Jeff Nauss <jnauss(a)accelrys.com> Content-Type: text/plain; charset="US-ASCII" Date: Wed, 28 Feb 2007 12:12:30 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss~~accelrys.com] Accelrys Inc. are holding the following training workshops during April. These events are designed to help you get more value from your Accelrys software, helping you to better accomplish your research goals. For the on-line presentations, the price is $175 per three hour session for all customers. ONLINE TRAINING Introduction to Materials Studio 2 Apr (4pm GMT) Scripting in Materials Studio 3 Apr (8am GMT) Protein-Protein Docking with InsightII 4 Apr (7am PDT) InsightII to Discovery Studio Migration 5 Apr (7am PDT) Catalyst Migration 11 Apr (4pm GMT) Introduction to Discovery Studio 17 Apr (4pm GMT) Further details can be found on our website at http://www.accelrys.com/services/training/general/calendar.html. Please visit http://www.accelrys.com/services/training/ for a complete list of available workshops and opportunities. Questions regarding scheduling and content should be directed to workshops**accelrys.com -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training From owner-chemistry@ccl.net Wed Feb 28 19:19:00 2007 From: "Jan Labanowski janl()speakeasy.net" <owner-chemistry##server.ccl.net> To: CCL Subject: CCL: CCL will be lightly attended for the next two weeks Message-Id: <-33711-070228190656-9344-ev2HMXo8REvZ2fFoe0GeTw##server.ccl.net> X-Original-From: "Jan Labanowski" <janl*o*speakeasy.net> Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 01 Mar 2007 00:06:38 +0000 MIME-Version: 1.0 Sent to CCL by: "Jan Labanowski" [janl*|*speakeasy.net] Dear CCL, I wanted to warn you that I am flying for two weeks to Poland on Thu, March 1, and I will be far away from my basement, where the server.ccl.net runs. I was invited to give a talk at a Winter School ( http://biotka.mol.uj.edu.pl/zakopane2007/ , BTW, I love these marching cells...). My son Dominic (a high school junior) is around in case the "button" needs to be pushed, and he will try to moderate the list for newcommers, but expect delays (he is a busy fellow trying to collect points to qualify for some scholarship to a decent university that his father cannot afford, and he is not a computational chemistry type...). There may be something good coming from this trip for CCL, though. I have a preliminary agreement to place a mirror of CCL in one of Poland's leading networking organization. If this works out, the CCL will have a mirror and the bandwidth 10 or maybe 100 times the current one (this is especially important for CCL archives that house a lot of stuff). Of course, it all depends if OUR dear people that keep us safe, do not pulverize the motherboard combo (and the hard drive with the preinstalled CCL on it) when checking my luggage. Moreover, there is no win... If you wrap stuff well for protection against conveyor abuse, you are guaranteed that it will be messed up by sniffers. Keep your fingers crossed... Best to you all... Time to start packing and checking if I am not over the new 50lb limit for suitcases... (I am also carrying tons of sheet music for my musically challenged sister in Poland, and many of "something symbolic" for my family). Jan Your CCL watchdog rather than Guarding Angel... P.S. CCL has won a dubious recognition of being a trusted service among spammers and virus infected Windoz zombies (the highest honors coming from those who really know). For this reason the CCL email address is often found on the From: line of spam/virus messages. Note, the From: line of the message is the easiest thing to fake. It is easy to check that they are phoney. Look at your message header and if the first Received: line does not say: 66.93.212.15 it did not come from here. If it came (and to my knowledge it did not come from here for many years) let me know promptly, since it would mean that CCL had been cracked. While it would hurt my ego a lot, I would really prefer to know it earlier than later and save you from all those winning notices, business opportunities, penetrating photos, and cheap and exciting medications (not even mentioning the stinking phish). You already get more than you need without my help. And you see... The problem is that I cannot hide the CCL List email address since you would not post your excellent questions and answers (no pun intended)...