From owner-chemistry@ccl.net Fri Sep 17 02:19:00 2010 From: "Thomas Gkourmpis thomas.gkourmpis**borealisgroup.com" To: CCL Subject: CCL:G: Solvation Calculation Problem Message-Id: <-42781-100917021740-29947-iXdCCVzPCADFWmys5e0WPQ:server.ccl.net> X-Original-From: "Thomas Gkourmpis" Date: Fri, 17 Sep 2010 02:17:38 -0400 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis_+_borealisgroup.com] Hello everyone I am having a problem trying to perform optimisation and frequency calculations in Gaussian03/09W in radicals in the presense of solvent (heptane). I have tried a number of radicals like CH3* and everything worked fine. I got the results and they seem reasonable. Every time I am trying to do the same calculation on oxygen based radicals like a tertbutoxy radical for example the whole calculation crashes due to lack of convergence. (this happens with all solvation models available in Gaussian) My input parameters are: %nprocshared=4 %chk=C:\Software\G09W\Projects\Tertbutoxy Radical with Solvent Opt.chk #p opt freq=noraman ub3lyp/6-311g(d,p) scrf=(solvent=heptane) geom=connectivity Am I doing something wrong here? How can I make sure my structure converges to something meaningful? Any ideas or suggestions will be more than welcome. Thanks a lot in advance Thomas Gkourmpis From owner-chemistry@ccl.net Fri Sep 17 08:25:00 2010 From: "Jozsef Csontos jcsontos.lists],[gmail.com" To: CCL Subject: CCL: Capping termini - protein modeling Message-Id: <-42782-100917051429-9841-v7BNGxGL3Ap5YFxaW15iGQ!A!server.ccl.net> X-Original-From: Jozsef Csontos Content-Type: multipart/alternative; boundary="------------090707060609000700010802" Date: Fri, 17 Sep 2010 11:14:15 +0200 MIME-Version: 1.0 Sent to CCL by: Jozsef Csontos [jcsontos.lists===gmail.com] This is a multi-part message in MIME format. --------------090707060609000700010802 Content-Type: text/plain; charset=UTF-8; format=flowed Content-Transfer-Encoding: 7bit Maura, capping is important if the residues, which are close to the place of truncation (consequently to the capping), have a non-negligible effect on the property you are interested in. Non-appropriate capping groups can generate artificial interactions which would not be present in the native, non-truncated protein and cover-up what really happens in the native peptide region. You might want to read the following paper about different capping options. http://dx.doi.org/10.1002/qua.21553 Abstract: The accuracy of the determination of the energy of interaction between Phe20 and the Pro5-Thr6-Tyr7-Pro8 complex inside the hydrophobic core of avian pancreatic polypeptide was investigated using three capping strategies for molecular fractionation with conjugated caps and DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. The most accurate determination resulted from acetylation of the a-amino group combined with methyl amidation of the a-carbonyl group, with relative deviations less than 10%. Combinations of hydrogenation of the a-amino group with the replacement of the a-carbonyl group with a hydrogen and the hydrogenation of the a-amino group with methylation of the a-carbonyl group were less accurate, leading to relative deviations up to 35%. Choice of capping methods depends on the structural features of the polypeptide system, the desired accuracy, and the available computational resources. Best, Jozsef On 09/16/2010 09:16 AM, Maura Mooney mmooney05,+,qub.ac.uk wrote: > Sent to CCL by: "Maura Mooney" [mmooney05%a%qub.ac.uk] > Hi, > > My question regards peptide caps. I have a few proteins (~25kDa) in which the first and last few residues are truncated. In what circumstances should I cap the protein termini, and apart from stability in small alpha helices, why should we cap protein termini? > > Thanx,> > > --------------090707060609000700010802 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Maura,

capping is important if the residues, which are close to the place of truncation (consequently to the capping), have a non-negligible effect on the property you are interested in. Non-appropriate capping groups can generate artificial interactions which would not be present in the native, non-truncated protein and cover-up what really happens in the native peptide region.

You might want to read the following paper about different capping options.

http://dx.doi.org/10.1002/qua.21553

Abstract: The accuracy of the determination of the energy of interaction between Phe20 and the Pro5-Thr6-Tyr7-Pro8 complex inside the hydrophobic core of avian pancreatic polypeptide was investigated using three capping strategies for molecular fractionation with conjugated caps and DFT quantum chemical calculations at the BHandHLYP/cc-pVTZ level of theory. The most accurate determination resulted from acetylation of the a-amino group combined with methyl amidation of the a-carbonyl group, with relative deviations less than 10%. Combinations of hydrogenation of the a-amino group with the replacement of the a-carbonyl group with a hydrogen and the hydrogenation of the a-amino group with methylation of the a-carbonyl group were less accurate, leading to relative deviations up to 35%. Choice of capping methods depends on the structural features of the polypeptide system, the desired accuracy, and the available computational resources.

Best,
Jozsef

On 09/16/2010 09:16 AM, Maura Mooney mmooney05,+,qub.ac.uk wrote: 
Sent to CCL by: "Maura  Mooney" [mmooney05%a%qub.ac.uk]
Hi,

My question regards peptide caps. I have a few proteins (~25kDa) in which the first and last few residues are truncated. In what circumstances should I cap the protein termini, and apart from stability in small alpha helices, why should we cap protein termini?

Thanx,E-mail to subscribers: CHEMISTRY++ccl.net or use:
      http://www.ccl.net/cgi-bin/ccl/send_ccl_message

E-mail to administrators: CHEMISTRY-REQUEST++ccl.net or use
      http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtml

Before posting, check wait time at: http://www.ccl.net

Job: http://www.ccl.net/jobs 
Conferences: http://server.ccl.net/chemistry/announcements/conferences/

Search Messages: http://www.ccl.net/chemistry/searchccl/index.shtmlhttp://www.ccl.net/spammers.txt

RTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
--------------090707060609000700010802-- From owner-chemistry@ccl.net Fri Sep 17 09:00:00 2010 From: "Ol Ga eurisco1:+:pochta.ru" To: CCL Subject: CCL:G: Solvation Calculation Problem Message-Id: <-42783-100917082725-32566-bLHr8ftGhfwSK+wGYgxfQQ!^!server.ccl.net> X-Original-From: "Ol Ga" Date: Fri, 17 Sep 2010 08:27:24 -0400 Sent to CCL by: "Ol Ga" [eurisco1-x-pochta.ru] Dear Thomas Gkourmpis, To achieve SCF convergence especially for radicals I would suggest you to add in route section SCF keyword like SCF(XQC,maxcycle=512,vshift=150) Sincerely, Ol Ga PS: geom=connectivity is not required for DFT. -------------------------------------------------- > From: "Thomas Gkourmpis thomas.gkourmpis**borealisgroup.com" Sent: Friday, September 17, 2010 10:17 AM To: "Ga, Ol " Subject: CCL:G: Solvation Calculation Problem > > > Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis_+_borealisgroup.com] > Hello everyone > > I am having a problem trying to perform optimisation and frequency calculations in Gaussian03/09W in radicals in the presense of solvent (heptane). > > I have tried a number of radicals like CH3* and everything worked fine. I got the results and they seem reasonable. Every time I am trying to do the same calculation on oxygen based radicals like a tertbutoxy radical for example the whole calculation crashes due to lack of convergence. (this happens with all solvation models available in Gaussian) > > My input parameters are: > > %nprocshared=4 > %chk=C:\Software\G09W\Projects\Tertbutoxy Radical with Solvent Opt.chk > #p opt freq=noraman ub3lyp/6-311g(d,p) scrf=(solvent=heptane) > geom=connectivity > > Am I doing something wrong here? How can I make sure my structure converges to something meaningful? Any ideas or suggestions will be more than welcome. > > Thanks a lot in advance > > Thomas Gkourmpis > > > > From owner-chemistry@ccl.net Fri Sep 17 11:02:01 2010 From: "David S. Hollman dhollman^ccqc.uga.edu" To: CCL Subject: CCL: StackOverflow-like Q&A site for computational chemistry Message-Id: <-42784-100917101810-8317-R0KHU4pzMwOlgk/OYlGfDA[a]server.ccl.net> X-Original-From: "David S. Hollman" Date: Fri, 17 Sep 2010 10:18:09 -0400 Sent to CCL by: "David S. Hollman" [dhollman===ccqc.uga.edu] Many of you are probably familiar with the popular programming and computer science question and answer site stackoverflow.com. Like many of these types of websites, (yahoo answers, etc.), StackOverflow allows users to post questions or answer questions that others have asked, creating a searchable database of common problems that programmers have. The difference is that StackOverflow has focused on creating a community of experts, which effectively filters out the high-schooler-homework-help types of questions. The StackOverflow team has recently launched a new site called StackExchange, where users are encouraged to suggest topics for new StackOverflow-like websites. Any topics that make it through the screening process become dedicated websites hosted, maintained, and paid for by the StackOverflow team. In order to establish that there is a large enough online community of experts to make the site viable, a proposed StackExchange topic first needs 60 "followers" who are interested in the topic. Then it needs 200 people to "commit" to participated in a private beta before they launch a website. I have recently proposed a Computational Chemistry site in Area51, which is what they call the StackExchange staging area. I would appreciate it if people on CCL would take a couple of minutes to "follow" this proposal so that we can move into the next step in the process. The URL of the proposal is: http://area51.stackexchange.com/proposals/19727/computational-chemistry?referrer=Di3XslRnv5x6zBRaqbsfBg2 If you already have a StackOverflow account, then following the proposal is as easy as associating your stackoverflow.com account with Area51 and clicking "follow." Otherwise, particularly if you have a Google, Yahoo, or other OpenID account, signing up for StackExchange is just as easy. Don't worry, none of the StackExchange sites send any sort of unsolicited e-mail or anything, and of course all of this is completely free. Thanks! David S. Hollman Center for Computational Quantum Chemistry University of Georgia Athens, GA 30602 dhollman,,ccqc.uga.edu From owner-chemistry@ccl.net Fri Sep 17 15:46:00 2010 From: "Joy Ku joyku(_)stanford.edu" To: CCL Subject: CCL: OpenMM Zephyr 2.0 Available with Explicit Solvent and OpenCL Support Message-Id: <-42785-100917154427-11974-DqdveY7D7AWtyZekbSnvtA-,-server.ccl.net> X-Original-From: "Joy Ku" Date: Fri, 17 Sep 2010 15:44:23 -0400 Sent to CCL by: "Joy Ku" [joyku],[stanford.edu] Simbios is excited to announce the release of OpenMM Zephyr 2.0. OpenMM Zephyr is a freely available molecular simulation application with an easy-to-use graphical user interface and GPU-acceleration capabilities. Combining the molecular dynamics software GROMACS with the accelerated calculations possible with the OpenMM library and the visualization capabilities of VMD, OpenMM Zephyr provides a way to quickly get started with molecular dynamic simulations. In this new version, you are able to run explicit solvent simulations from the graphical user interface. In addition to NVIDIA GPUs, OpenMM Zephyr now also supports OpenCL on all platforms, including ATI GPU boards. You can download the latest version from http://simtk.org/home/zephyr. From owner-chemistry@ccl.net Fri Sep 17 21:20:00 2010 From: "Li Chen Lichen2x---gmail.com" To: CCL Subject: CCL: Calculation of IV curve and Transmission spectra Message-Id: <-42786-100917211411-31618-KIOz1CjwtzHKBtg7Z07rEw{=}server.ccl.net> X-Original-From: "Li Chen" Date: Fri, 17 Sep 2010 21:14:10 -0400 Sent to CCL by: "Li Chen" [Lichen2x-x-gmail.com] Dear All Is there a free (or cheep) program for calculation of current-voltage curve and transmission spectra for organic molecule? It is better if the program work under windows platform. Your help would be be greatly appreciated Regards Li