From owner-chemistry@ccl.net Tue Jan 24 12:57:00 2006 From: "Christofer Tautermann hannyho*_*yahoo.com" To: CCL Subject: CCL: Assessment of the quality of a Homology Model Message-Id: <-30608-060124112625-2702-99X3dMaXVpxz8BXrrsRS5g+/-server.ccl.net> X-Original-From: "Christofer Tautermann" Sent to CCL by: "Christofer Tautermann" [hannyho#%#yahoo.com] Hi! I am builing homology models of proteins (using different programs - e.g. Modeller, MOE) by comparative modeling. The output is a huge amount of models for the same protein - but the difficulty is to find the "best" structure which is closest to the target. I am using several protein-structure checks (WhatCheck, procheck, ...) and they help to discard some unreasonable models, but they don't help finding the best model. Are there any proposals how to pick the model which is closest to the native structure - or at least some of the "better" models? Thanks for your help Christofer From owner-chemistry@ccl.net Tue Jan 24 14:47:00 2006 From: "Yingbin Ge yingbin.ge++gmail.com" To: CCL Subject: CCL: QMMM for pyrolytic carbon Message-Id: <-30609-060124144518-30622-QFVkWDEHn2hdPvFzobcALA],[server.ccl.net> X-Original-From: Yingbin Ge Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 24 Jan 2006 12:49:22 -0600 MIME-Version: 1.0 Sent to CCL by: Yingbin Ge [yingbin.ge-#-gmail.com] Hi there, I am studying heterogeneous reactions between gas phase species such as SiCl2 and pyrolytic C surface. My final goal is to model the beta-SiC deposition and growth on pyrocarbon. Since the structure of the pyrolytic C resembles that of graphite, I plan to investigate reactions between SiCl2 and a graphene sheet as a starting point. However the graphene is a highly conjugated system. It seems to me that at least 7 rings (1 middle and 6 surrounding rings) should be treated as the QM part, which is almost impossible for any method with modest accuracy (I was thinking of using CCSD(T)//UMP2/aug-cc-pVDZ level of theory). I look forward to getting your advice! Yingbin From owner-chemistry@ccl.net Tue Jan 24 19:48:00 2006 From: "H J Fan hjfan(_)pvamu.edu" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30610-060124194658-27452-kJWn53U4EtQKeaOM5hrX0A(~)server.ccl.net> X-Original-From: "H J Fan" Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] Hi, I once was a fan of Gaussian. Due to recent headache of License terms and extra long delay from Gaussian, I am seeking the advice on comparable software that I can purchase to do the similar calculations with a decent graphic interface. I am aware of free GAMESS but it lacks of graphic interface. Does MWCHEM have an interface? From Gaussian website, it has a price tag about 7,000 total for site license of both Gaussian and GView together. With that price, what kind of software can I buy? even better with site license though not necessary. Not to offend other Gaussian fan, here is the story: Gaussian basically reject my purchase order because there are some typical words on the back of the purchase order, called terms. They want my school to sign a blank agreement about license terms, and I am sure that freaks out my officials since normally, when they put in an order, nobody makes such a big fuss about what's written behind the purchase order, since the terms behind has no conflict with whatever the company wants. With this blank term asked by Gaussian, my purchase order has been stuck somewhere since Nov 26, last year. Unlike Spartan, once I scan the order to them, I got the software two days later, no questions asked. And I can assure everyone out there, I have no intention to do anything illegal about Spartan with or without terms behind the purchase order. Remembered a big hot discussion about Gaussian not so far ago. SIGH... I really should have listened. So I am looking for advice on the softare to spend this 7,000, probably more. Thanks in advance. From owner-chemistry@ccl.net Tue Jan 24 23:17:00 2006 From: "Nuno A.G. Bandeira nuno.bandeira,,ist.utl.pt" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30611-060124231534-22211-4WsU4UxCjX2QjprIVdbniA!=!server.ccl.net> X-Original-From: "Nuno A.G. Bandeira" Sent to CCL by: "Nuno A.G. Bandeira" [nuno.bandeira,,ist.utl.pt] In terms of versatility, NWChem is close to Gaussian but there are still no analytic frequencies yet you'll have to stick to numerical runs. Some basic differences here and there but it's a good competitor considering it's free. Problem is the GUI. There aren't all that many QM codes coupled with GUIs. Spartan is indeed one exception and it's got the best model builder I've seen yet. NWChem has a GUI associated with it but it only runs in Linux. It's called Ecce. Esthetically it's similar to GaussView and you can also run it as a server to monitor jobs on different machines. ADF is a very good software and it has a GUI to go with it but it's not at all versatile. It all depends on what kind of calculations you want to run. One (very expensive) option you could consider is to purchase DMol3 because it's fully inbuilt (but you can also run it from the command prompt) in a GUI called Materials Studio (aka Cerius2) from the UK based company Accelrys. I've never used it but I've browsed through their website quite a few times and if you can get it it would definitely be a deluxe addition to your computational tools. It runs in Windows, need I say more ? See this http://www.accelrys.com/products/mstudio/modeling/quantumandcatalysis/dmol3.html hope this helps, -- Nuno A. G. Bandeira, AMRSC Graduate researcher and molecular sculptor Inorganic and Theoretical Chemistry Group, Faculty of Science University of Lisbon - C8 building, Campo Grande, 1749-016 Lisbon,Portugal http://cqb.fc.ul.pt/intheochem/nuno.html Doctoral student !A! IST,Lisbon -- From owner-chemistry@ccl.net Tue Jan 24 23:54:00 2006 From: "Dr. Seth Olsen s.olsen1:-:uq.edu.au" To: CCL Subject: CCL:G: comparable software to Gaussian Message-Id: <-30612-060124221326-31263-iBf92X4AFubLX7Dx+3n0BQ!A!server.ccl.net> X-Original-From: "Dr. Seth Olsen" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 25 Jan 2006 13:13:16 +1000 MIME-Version: 1.0 Sent to CCL by: "Dr. Seth Olsen" [s.olsen1\a/uq.edu.au] If you obtain a license for NWChem, it should also include a lisence for the ECCE software, which provides a graphical interface. GAMESS results can, in principle, be visualized quite well in MOLEKEL. I am sure that there are other graphical programs which accept GAMESS output as well. H J Fan hjfan(_)pvamu.edu wrote: >Sent to CCL by: "H J Fan" [hjfan||pvamu.edu] >Hi, I once was a fan of Gaussian. Due to recent headache of License terms and extra long delay from Gaussian, I am seeking the advice on comparable software that I can purchase to do the similar calculations with a decent graphic interface. > >I am aware of free GAMESS but it lacks of graphic interface. Does MWCHEM have an interface? From Gaussian website, it has a price tag about 7,000 total for site license of both Gaussian and GView together. With that price, what kind of software can I buy? even better with site license though not necessary. > >Not to offend other Gaussian fan, here is the story: Gaussian basically reject my purchase order because there are some typical words on the back of the purchase order, called terms. They want my school to sign a blank agreement about license terms, and I am sure that freaks out my officials since normally, when they put in an order, nobody makes such a big fuss about what's written behind the purchase order, since the terms behind has no conflict with whatever the company wants. With this blank term asked by Gaussian, my purchase order has been stuck somewhere since Nov 26, last year. Unlike Spartan, once I scan the order to them, I got the software two days later, no questions asked. And I can assure everyone out there, I have no intention to do anything illegal about Spartan with or without terms behind the purchase order. > >Remembered a big hot discussion about Gaussian not so far ago. SIGH... I really should have listened. So I am looking for advice on the softare to spend this 7,000, probably more. Thanks in advance.> > > > >