From owner-chemistry@ccl.net Thu Apr 5 04:27:00 2007 From: "Ulrike Salzner salzner() fen.bilkent.edu.tr" To: CCL Subject: CCL:G: Hardware Message-Id: <-33968-070405042125-18269-VNC8NBRcYCNG1/5h8oTS9w++server.ccl.net> X-Original-From: Ulrike Salzner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 05 Apr 2007 11:20:37 +0300 MIME-Version: 1.0 Sent to CCL by: Ulrike Salzner [salzner(-)fen.bilkent.edu.tr] Hello, I am planning to spend an amount of about $100000 on new computers for quantum chemical calculations. I will use mainly G03 and my main interest is currently in TDDFT calculations of large systems 100+ atoms. I am wondering what is the best set up to get as much performance for the $ as possible. I am thinking of a PC cluster. Is it better to buy complete PCs or is a blade server an option? Or is it better to switch to work stations? Another questions relates to memory. Normaly people suggest to get as much as possible. However, as was discussed recently on CCL, more memory gives a huge speed-up, if the calculation can switch to in-core management of the intergrals. I think there is no way for large systems to do that. I found that G03 jobs run fastest with just enough memory and slow down, the more memory is requested. I tested this with relatively small jobs, so I may be wrong. With a cluster I made the following expereience. I ran jobs that work fine on a single PC with 1GB of RAM, requesting 700MB. Trying the same job on three identical PCs requesting 700MB, Linda switched on node because of lack of memory. How much memory would I need to run such a job on a cluster using all nodes? Thanks for any suggestions. Ulrike From owner-chemistry@ccl.net Thu Apr 5 05:04:00 2007 From: "Stefan.Guessregen*o*sanofi-aventis.com" To: CCL Subject: CCL: REMINDER: 21st "Darmstadt" Molecular Modelling Workshop - May 15-16, 2007 in Erlangen Message-Id: <-33969-070405045310-30290-Xl5mkCrDxRgCuVAzPdoqhQ*o*server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 5 Apr 2007 10:52:23 +0200 MIME-Version: 1.0 Sent to CCL by: [Stefan.Guessregen/a\sanofi-aventis.com] Dear Colleagues, This is just to remind you that the deadline for registration and submission of abstracts to the 21st "Darmstadt" Molecular Modeling Workshop is approaching rapidly! Best regards, Stefan Guessregen ======================================================================== ============================= 21st "Darmstadt" Molecular Modeling Workshop Computer-Chemie-Centrum, 91052 Erlangen, Germany Tuesday, May 15 - Wednesday, May 16, 2007 Dear Colleagues, I would like to bring to your attention that the 21st "Darmstadt" Molecular Modeling Workshop will be taking place in Erlangen on May 15th and 16th 2007. The goal of the Workshop is to give young scientists, especially PhD students and Post-Docs, the chance to present their current research, industrial colleagues are able to gain an overview about ongoing academic research. Contributions from all areas of molecular modelling, life sciences to materials, are highly welcome. We are pleased to announce that the following scientists have agreed to give plenary lectures: Prof. Thierry Langer (University of Innsbruck) Prof. Wilfred van Gunsteren (ETH Zurich) For any further information regarding the program, registration, location, and accomodation, please refer to the following website: http://www.chemie.uni-erlangen.de/ccc/darmstadt.html The deadline for registration is 13th April 2007. Best regards Stefan Guessregen Dr. Stefan Guessregen Sanofi-Aventis Deutschland GmbH Scientific & Medical Affairs / Drug Design Industriepark Hoechst, Building G 878 D-65926 Frankfurt am Main Germany Phone: +49 (69) 305 26 616 Fax: +49 (69) 305 942 333 E-Mail: stefan.guessregen*aatt*sanofi-aventis.com ************************************************************************ ************************************************************************ ************** Sanofi-Aventis Deutschland GmbH * Sitz der Gesellschaft: Frankfurt am Main * Handelsregister: Frankfurt am Main, Abt. B Nr. 40661 Vorsitzender des Aufsichtsrats: Hanspeter Spek - Geschaeftsfuehrer: Dr. Heinz-Werner Meier (Vorsitzender), Dr. Matthias Braun, Herve Gisserot, Dieter Kohl, Prof. Dr. Dr. Werner Kramer, Dr. Martin Siewert ************************************************************************ ************************************************************************ ************** From owner-chemistry@ccl.net Thu Apr 5 08:40:00 2007 From: "Tae-Rae Kim eigenskim^-^gmail.com" To: CCL Subject: CCL: IRC calculation using GAMESS Message-Id: <-33970-070403232115-16859-5QGIKkhQf/0u6MisCydo7g()server.ccl.net> X-Original-From: "Tae-Rae Kim" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 4 Apr 2007 11:26:02 +0900 MIME-Version: 1.0 Sent to CCL by: "Tae-Rae Kim" [eigenskim^^^gmail.com] > Problem 1): > If I set up my IRC calculation using a small number for NPOINT, the entire IRC is not found. When I try to restart it using the restart information provided by the program in the *.dat file, I get the message: > > RADIUS IN CIRCLE OPTIMIZATION 0.0067834 DEVIATES SIGNIFICANTLY FROM CONSTRAIN CONDITION 0.0050000 > IT IS POSSIBLE THAT THE NEXT IRC POINT IS CLOSE TO A MINIMUM > > I find it to be extremely unlikely that the system is near a minimum at exactly the point which corresponds to my setting of NPOINT. Does anybody know the fix for this problem? I guess what I am asking is how does one resart an IRC calculation correctly in GAMESS? I do not rely on restart options. It can be very nervous sometimes. Instead, I copy required informations (groups punched in .dat or .irc file) and paste it into input file. Some options should be added to let GAMESS read the groups. > Problem 2) > When I ran into problem 1, I increased NPOINT and let the calculation run longer. Then eventually the calculation stopped with the same message (but this time at a point smaller than my setting of NPOINT): > > RADIUS IN CIRCLE OPTIMIZATION 0.0067834 DEVIATES SIGNIFICANTLY FROM CONSTRAIN CONDITION 0.0050000 > IT IS POSSIBLE THAT THE NEXT IRC POINT IS CLOSE TO A MINIMUM > > This time it may be true that the system is near a minimum, I dont know. When I use the MacMolPlt-program and look at the potential enenrgy surface for the IRC-calculation the system appears NOT to be near a minimum. The potential energy surface is not curved at all for the last points in the IRC-calculation which is in my mind what should happen near the minimum. However, I can be wrong about this. Does anybody know how I should continue to reach the true minimum? I don't think I can restart using the information provided by the program because then I will run into problem 1. I think that the curve needs not be rolled up. In principle, dynamic path should oscillate around minimum. But the program exits when the system reaches near local minimum, before oscillation. -- Kim, Tae-Rae Dycube Lab. (Prof. S.Shin) Department of Chemistry Seoul Natl. Univ., South Korea From owner-chemistry@ccl.net Thu Apr 5 09:49:01 2007 From: "Herbert Fruchtl herbert.fruchtl(!)st-andrews.ac.uk" To: CCL Subject: CCL:G: Hardware Message-Id: <-33971-070405093849-18338-mx7/zdeHAjw+cfpaSTCQpQ##server.ccl.net> X-Original-From: Herbert Fruchtl Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 05 Apr 2007 14:38:07 +0100 MIME-Version: 1.0 Sent to CCL by: Herbert Fruchtl [herbert.fruchtl##st-andrews.ac.uk] Dear Ulrike, $100k will buy you a serious machine, and you don't want to build that > from PCs (I assume you mean "real" desktop PCs). It makes more sense to buy something rack-mounted. You will need a dedicated room with Aircondition; these things produce a lot of heat (and noise). Probably not a blade server, because you need large and fast local disks for most QM calculations. Processor-wise, it's a tossup between AMD Opteron and Intel Xeon. The Xeon is faster as an individual processor, the Opteron has the better memory architecture and will scale better if you run SMP parallel (which is what you want with Gaussian; forget about Linda...). Ask some vendors to run benchmarks (real calculations, and in parallel) and look at their prices. You will get the best price/performance ratio with 4-core systems (dual processor, dual core), but if you want to run large SMP calculations, you may want to look at 8-core nodes. Don't buy less memory than 2GB/core. You may not need it in every calculation (G03 does indeed get slower if you allow it to use too much), but sometimes you will need it. If you want to run really big parallel calculations, you may want to look at a low latency network (Myrinet, Infiniband, InfiniPath..), but this is fairly expensive, and you should check if your programs can actually use it. Have a look at http://www.beowulf.org/, sign up to their mailing list and have a look at the mailing list archives for all cluster related questions. If you want to run really large calculations on the whole cluster, have a look at NWChem. Performance on one (or a few) processors is abysmal compared to Gaussian or other programs, but it scales good (often superlinear, because you use more memory on more nodes, and the implementation is truly distributed-memory, so you actually make use of all that memory). It's free, and fairly easy to use. Servus, Herbert Ulrike Salzner salzner() fen.bilkent.edu.tr wrote: > > Sent to CCL by: Ulrike Salzner [salzner(-)fen.bilkent.edu.tr] > Hello, > I am planning to spend an amount of about $100000 on new computers for > quantum chemical calculations. I will use mainly G03 and my main > interest is currently in TDDFT calculations of large systems 100+ atoms. > I am wondering what is the best set up to get as much performance for > the $ as possible. I am thinking of a PC cluster. Is it better to buy > complete PCs or is a blade server an option? Or is it better to switch > to work stations? > > Another questions relates to memory. Normaly people suggest to get as > much as possible. However, as was discussed recently on CCL, more memory > gives a huge speed-up, if the calculation can switch to in-core > management of the intergrals. I think there is no way for large systems > to do that. I found that G03 jobs run fastest with just enough memory > and slow down, the more memory is requested. I tested this with > relatively small jobs, so I may be wrong. With a cluster I made the > following expereience. I ran jobs that work fine on a single PC with 1GB > of RAM, requesting 700MB. Trying the same job on three identical PCs > requesting 700MB, Linda switched on node because of lack of memory. How > much memory would I need to run such a job on a cluster using all nodes? > > Thanks for any suggestions. > Ulrikehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Herbert Fruchtl EaStCHEM Fellow School of Chemistry University of St Andrews From owner-chemistry@ccl.net Thu Apr 5 10:24:00 2007 From: "errol lewars elewars() trentu.ca" To: CCL Subject: CCL:G: ts in gaussian Message-Id: <-33972-070404182223-16781-0Oua38rbQh4imOlDcufFfA . server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 04 Apr 2007 17:20:53 -0400 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars_-_trentu.ca] 2007 April 4 Hello, I'm not sure what you mean by linear hydrocarbons (acyclic alkanes?), but try this input transition state, for OH radical abstraction of a terminal H from propane: %chk=2007April04_OHradTS %Mem=100000000 %rwf=a,240mw,b,240mw,c,240mw,d,240mw,e,240mw,f,240mw,g,240mw,h,-1 # HF/3-21G Opt(TS, NoEigenTest, MNDOFC, MaxCycle=99) Freq Maxdisk=15360MB Input: HO...H...CH2-CH2-CH3 TS, AM1 geom 0 2 H1 -0.000000000 0.000000000 -1.776142859 C2 0.536402118 -0.000000000 -0.603627600 H3 1.140000000 0.920000000 -0.620000000 H4 1.140000000 -0.920000000 -0.620000000 O5 -0.000000000 0.000000000 -3.071011831 H6 0.756928642 0.000000000 -3.326088110 C7 -0.579339646 -0.000000000 0.383570085 H8 -1.228000000 0.903000000 0.224000000 H9 -1.228000000 -0.903000000 0.224000000 C10 -0.000000000 0.000000000 1.798329610 H11 0.574800000 0.905000000 1.985000000 H12 0.574800000 -0.905000000 1.985000000 H13 -0.899922957 0.000000000 2.523801432 You should be able to modify this input for other alkanes, and to use other levels than HF/3-21G. I got it by building a guess TS using my chemical intuition, optimizing to a TS at the AM1 level, then adjusting the cartesian coordinates of the optimized geometry slightly to get exact Cs symmetry; with my builder there was a problem getting Cs sym for the _input_ structure, which would have been easier than hand tweaking, and I didn't want to mess with a Z-matrix. I used G03 but it should work with G98. E. Lewars ==== Aleksandra N rudnitskaya aleksandra.rudnit001[A]umb.edu wrote: >Sent to CCL by: "Aleksandra N rudnitskaya" [aleksandra.rudnit001^^umb.edu] >Hi, > >I work on the finding transitional states in reaction OH radical with linear hydrocarbons using everything in Gaussian 98. The reaction is >Hydrocarbon +OH = H2O + Radical. > >Ive already tried everything I known: >1. TS > opt=ts freq=noraman uhf/6-31+g >It does not work because program doesnt recognize imaginary frequency while it is there I checked it with frequency job; >2. No Eigen Test and 3. Eigenvalue follow > opt=(ts,noeigentest) freq=noraman uhf/6-31+g > opt=(ts,ef) freq=noraman uhf/6-31+g >Those guys dont work also. As the results Ive usually either product or reactant which is far apart from another molecule (OH radical or water molecule). >3. QST2/QST3 > opt=(ts,qst2) freq=noraman uhf/6-31+g >Its extremely hard to predict geometry of both reactants and products to get TS. > >Question: > >I took my linear hydrocarbon, optimized it and got geometry of first reactant. >I did the same with OH radical and got the geometry of the second reactant. >I took out one of the hydrogens from the linear hydrocarbon and optimized it. Now Ive got product geometry. I did the optimization on the second product water. Now, the hardest part, HOW TO COMBINE MY HYDROCARBON WITH OH, what position OH should occupy relative to hydrocarbon? Ones I fond solution for that problem, I may produce similar geometry (angles and dihedral angles) for radical and water molecule. There are millions of possible combinations. From my experience, its extremely hard to find distances, angles, and especially dihedral angles that are close enough to transitional states. When I construct wrong structure or even one that is not close enough to solution, file usually crashes and molecules go apart. > >How do you solve this problem? Is there any algorithm, any book? > >Thank you very much. > >Aleksandra> > > > > From owner-chemistry@ccl.net Thu Apr 5 11:57:01 2007 From: "=?ISO-8859-1?Q?=D6d=F6n?= Farkas farkas%a%chem.elte.hu" To: CCL Subject: CCL:G: ts in gaussian Message-Id: <-33973-070405114013-13769-N0hdDhGilJ/+MtzPCn8uFw(_)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: Thu, 05 Apr 2007 17:39:04 +0200 Mime-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?=D6d=F6n?= Farkas [farkas[#]chem.elte.hu] Hi Aleksandra, It might also be a good idea to do some preliminary calculations to get as close to the TS as possible. Starting from a "complex" you can either increase the C-H bond, which will react, or decrease the O-H distance via relaxed scan using ModRedundant. If you are lucky you will get a highest energy point on the path which can be used as a starting geometry for TS search. Beside the trick others already advised you might also try using GDIIS. Good luck, Ödön On Wed, 2007-04-04 at 13:26 -0400, Aleksandra N rudnitskaya aleksandra.rudnit001[A]umb.edu wrote: > Sent to CCL by: "Aleksandra N rudnitskaya" [aleksandra.rudnit001^^umb.edu] > Hi, > > I work on the finding transitional states in reaction OH radical with linear hydrocarbons using everything in Gaussian 98. The reaction is > Hydrocarbon +OH = H2O + Radical. > > Ive already tried everything I known: > 1. TS > opt=ts freq=noraman uhf/6-31+g > It does not work because program doesnt recognize imaginary frequency while it is there I checked it with frequency job; > 2. No Eigen Test and 3. Eigenvalue follow > opt=(ts,noeigentest) freq=noraman uhf/6-31+g > opt=(ts,ef) freq=noraman uhf/6-31+g > Those guys dont work also. As the results Ive usually either product or reactant which is far apart from another molecule (OH radical or water molecule). > 3. QST2/QST3 > opt=(ts,qst2) freq=noraman uhf/6-31+g > Its extremely hard to predict geometry of both reactants and products to get TS. > > Question: > > I took my linear hydrocarbon, optimized it and got geometry of first reactant. > I did the same with OH radical and got the geometry of the second reactant. > I took out one of the hydrogens from the linear hydrocarbon and optimized it. Now Ive got product geometry. I did the optimization on the second product water. Now, the hardest part, HOW TO COMBINE MY HYDROCARBON WITH OH, what position OH should occupy relative to hydrocarbon? Ones I fond solution for that problem, I may produce similar geometry (angles and dihedral angles) for radical and water molecule. There are millions of possible combinations. From my experience, its extremely hard to find distances, angles, and especially dihedral angles that are close enough to transitional states. When I construct wrong structure or even one that is not close enough to solution, file usually crashes and molecules go apart. > > How do you solve this problem? Is there any algorithm, any book? > > Thank you very much. > > Aleksandra> > > -- 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 Thu Apr 5 12:29:01 2007 From: "MolSoft Training andy[#]molsoft.com" To: CCL Subject: CCL: Advanced ICM Workshop - Protein Structure and Drug Discovery - May 17th-18th 2007 Message-Id: <-33974-070404235614-26641-ZEtApOORuJwEnBkHTw+nog() server.ccl.net> X-Original-From: MolSoft Training Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Wed, 04 Apr 2007 15:28:56 -0700 MIME-Version: 1.0 Sent to CCL by: MolSoft Training [andy(0)molsoft.com] Molsoft LLC (www.molsoft.com) would like to invite you to an Advanced User ICM Workshop to be held on May 17th–18th 2007 in La Jolla, CA, USA. The course is suitable for chemists and biologists who have some prior experience with the MolSoft ICM desktop modeling environment. The workshop consists of lectures, demonstrations, and “hands-on” computational experiments. Lectures will include in-depth explanation of the algorithms and methods behind MolSoft's ICM technology. There will be emphasis placed on the ICM command language along with development of scripts for high throughput sequence analysis, modeling, and docking. In addition, the very latest ICM features will be showcased such as: fully-flexible receptor-ligand docking, flexible chemical superposition, pharmacophore derivation and molecular movie-making tools. Some of the topics covered in the workshop will include: - Sequence and Structure Analysis - Molecular Modeling and Simulations - Small Molecule and Protein-Protein Docking - Cheminformatics Tools - QSAR - Molecular Documents and Presentations (see: http://www.sgc.ox.ac.uk/iSee/downloads.html) Please see www.molsoft.com/training.html for more detailed information or E mail andy=-=molsoft.com or call (858) 625 2000 ext.108. MolSoft LLC is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. From owner-chemistry@ccl.net Thu Apr 5 13:37:02 2007 From: "Chun-Yi Sung juneyi1#,#yahoo.com.tw" To: CCL Subject: CCL:G: Visualizing NBO Message-Id: <-33975-070405131703-31416-uBzmZ/PfiyWeJUxBjZFh3w**server.ccl.net> X-Original-From: "Chun-Yi Sung" Date: Thu, 5 Apr 2007 13:16:59 -0400 Sent to CCL by: "Chun-Yi Sung" [juneyi1-$-yahoo.com.tw] Hi, I did some NBO analysis with G03, and I wonder if there is a way I can visualize those natural bond orbitals with GaussView or I should go for other visualization software like NBOview. thanks chunyi From owner-chemistry@ccl.net Thu Apr 5 14:37:01 2007 From: "Donald J. Keidel keided01:ucr.edu" To: CCL Subject: CCL: Animation of alpha helix wanted Message-Id: <-33976-070404215135-16930-pkzWBnxFKWBjKsteaQJt3w#%#server.ccl.net> X-Original-From: "Donald J. Keidel" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Wed, 4 Apr 2007 18:12:37 -0700 MIME-Version: 1.0 Sent to CCL by: "Donald J. Keidel" [keided01**ucr.edu] I am looking for an animation that someone might have or know whwere to download that shows a protein going from primary structure to alpha helix. I wanted to use it in my course to illustrate how the hydrogen bonding pattern develops. I have searched the net with no luck. Thank you in advance for all suggestions. Don Keidel From owner-chemistry@ccl.net Thu Apr 5 16:33:00 2007 From: "Shivani Syal ssyal%x%purdue.edu" To: CCL Subject: CCL: qsar volume calculation using hyperchem/other software Message-Id: <-33977-070405151150-22508-Cm8e+CG48w7nrJaEuJP3jg],[server.ccl.net> X-Original-From: "Shivani Syal" Date: Thu, 5 Apr 2007 15:11:46 -0400 Sent to CCL by: "Shivani Syal" [ssyal[-]purdue.edu] Hi everyone, I'm trying to write an excel macro/hcl script to automate solvent-excluded volume calculations using hyperchem but I'm having errors running it. Hperchem is not executing simple commands like 'qsar-property volume' using either DDE (via excel) or hcl scripts. In short, it is opening the dialog box but not changing the default option and performing the calculation. Does anyone have experience with a similar issue or know if such a functionality (doing batch calculations using the qsar module) is even possible in hyperchem? If not, can someone recommend a reliable software/program which gives the flexibility of computing volumes for different probe radii.(I'm not posting my script here for brevity reasons, but would be glad to do do if someone has any experience with the same). Thanks, Shivani From owner-chemistry@ccl.net Thu Apr 5 17:19:01 2007 From: "Ralf Tonner tonner*_*chemie.uni-marburg.de" To: CCL Subject: CCL:G: Visualizing NBO Message-Id: <-33978-070405170529-23574-Z5aO9c0AjjmDEDWTgx5RBw:+:server.ccl.net> X-Original-From: Ralf Tonner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Thu, 05 Apr 2007 22:26:49 +0200 MIME-Version: 1.0 Sent to CCL by: Ralf Tonner [tonner]=[chemie.uni-marburg.de] Dear chunyi, I do not know if these programs are able to do this but Molekel shows this capability (www.cscs.ch/molekel) - at least the "old" version 4.3. You have to conduct the Gaussian03/NBO-calculation and include "pop=nboread" and "gfoldprint" in the input-section. After the molecule specification you have to add the following lines: $NBO plot $END which will be read by the built-in NBO-module. You will find several files in your directory after the calculation has finished. FILE.37 is the one with the NBOs. Then you have to modify the Gaussian03-Output slightly as described earlier on this list: Replace "Gaussian 03" by "Gaussian 98" in the lines following the Gaussian reference list: Before change: ****************************************** Gaussian 03: SYSTEM 13-Oct-2005 DATE ****************************************** After change: ***************************************** Gaussian 98: SYSTEM 13-Oct-2005 DATE ****************************************** Now, you can open the G03-output with molekel and choose in the menu "Load --> nbo orb" the respective FILE.37. The option "Compute --> Orbital" gives a menu where you can choose the desired orbital for visualization. Ordering is equivalent to the NBO-summary section in the Gaussian-Output. Hope this helps Ralf. Chun-Yi Sung juneyi1#,#yahoo.com.tw schrieb: > Sent to CCL by: "Chun-Yi Sung" [juneyi1-$-yahoo.com.tw] > Hi, > > I did some NBO analysis with G03, and I wonder if there > is a way I can visualize those natural bond orbitals with > GaussView or I should go for other visualization software like > NBOview. > > thanks > > chunyi> > > > From owner-chemistry@ccl.net Thu Apr 5 17:49:01 2007 From: "ysubboti|ucalgary.ca" To: CCL Subject: CCL:G: Visualizing NBO Message-Id: <-33979-070405165216-17935-WoKUWJBQMOd5BtJBRK0JtQ _ server.ccl.net> X-Original-From: ysubboti-*-ucalgary.ca Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 5 Apr 2007 14:52:01 -0600 (MDT) MIME-Version: 1.0 Sent to CCL by: ysubboti^ucalgary.ca Hi Chunyi! Actually you can do it easily with any program reading CHK/FCHK files to visualize orbitals. You can find how to do it here: http://educ.gaussian.com/visual/Orbs/index.htm and here with GaussView: http://educ.gaussian.com/visual/Orbs/html/OrbsGaussView.htm. Just be sure that you have put in the line SaveNBOs keyword to save natural bond orbitals in the checkpoint file . Please take a look at gaussian manual to check how to control nbo module and for some other options. Good luck, Julia > > Sent to CCL by: "Chun-Yi Sung" [juneyi1-$-yahoo.com.tw] > Hi, > > I did some NBO analysis with G03, and I wonder if there > is a way I can visualize those natural bond orbitals with > GaussView or I should go for other visualization software like > NBOview. > > thanks > > chunyi> > > > > From owner-chemistry@ccl.net Thu Apr 5 18:56:01 2007 From: "Sachin Tyagi sachintyagi1 ~~ gmail.com" To: CCL Subject: CCL:G: gaussian error Message-Id: <-33980-070405184638-23680-3NSFZ6+BCRtBysZ7gxY3hw^server.ccl.net> X-Original-From: "Sachin Tyagi" Date: Thu, 5 Apr 2007 18:46:34 -0400 Sent to CCL by: "Sachin Tyagi" [sachintyagi1,+,gmail.com] Hi I am trying to do some gaussian calculations but I am getting the following errors.... 1. Inv2: IOpt= 1 Iter= 1 AM= 3.04D-15 Conv= 1.00D-12. Inverted reduced A of dimension 497 with in-core refinement. Isotropic polarizability for W= 0.000000 155.14 Bohr**3. End of Minotr Frequency-dependent properties file 721 does not exist. fclose of exec file failed. fclose of exec file failed.: Stale NFS file handle 2. Rotational constants (GHZ): 0.9383615 0.2268397 0.1971649 Standard basis: 6-31G (6D, 7F) There are 185 symmetry adapted basis functions of A symmetry. Integral buffers will be 262144 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned on. 185 basis functions, 459 primitive gaussians, 185 cartesian basis functions 71 alpha electrons 71 beta electrons nuclear repulsion energy 1420.4786747481 Hartrees. NAtoms= 29 NActive= 29 NUniq= 29 SFac= 7.50D-01 NAtFMM= 320 NAOKFM=F Big=F One-electron integrals computed using PRISM. NBasis= 185 RedAO= T NBF= 185 NBsUse= 185 1.00D-06 NBFU= 185 read from file GXX-Exec.Dat failed Returned from execl,istat=-1,errno=2! Returned from execl! I wonder if somebody could help me in fixing the problems. Thanks sachin From owner-chemistry@ccl.net Thu Apr 5 20:43:00 2007 From: "Kalju Kahn kalju*|*chem.ucsb.edu" To: CCL Subject: CCL: Animation of alpha helix wanted Message-Id: <-33981-070405201728-25707-njT3KtWNZeCtjSWrXTHl4Q,,server.ccl.net> X-Original-From: Kalju Kahn Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 05 Apr 2007 16:11:07 -0700 MIME-Version: 1.0 Sent to CCL by: Kalju Kahn [kalju(-)chem.ucsb.edu] Dear Donald, I do not have a movie of the "folding" but please see if the few animations or images available at http://www.chem.ucsb.edu/~molvisual/prot_struc.html meet your need. The animations are in MPG format but associated scenes can be readily created with PyMOL using the supplied PDB file and PyMOL script. You can then customize the visualization toward your on needs. We have also an animation illustrating the structure of DNA, cooperativity in hemoglobin, and induced fit in hexokinase. The whole site is at: http://www.chem.ucsb.edu/~molvisual/index.html Best wishes, Kalju ------------------- > > Sent to CCL by: "Donald J. Keidel" [keided01**ucr.edu] > > I am looking for an animation that someone might have or know whwere to > download that shows a protein going from primary structure to alpha helix. > I wanted to use it in my course to illustrate how the hydrogen bonding > pattern develops. I have searched the net with no luck. Thank you in > advance for all suggestions. > > Don Keidel> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ -+ > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry University of California, Santa Barbara From owner-chemistry@ccl.net Thu Apr 5 22:07:01 2007 From: "Warren DeLano warren-$-delsci.com" To: CCL Subject: CCL: Animation of alpha helix wanted Message-Id: <-33982-070405220241-25425-HgMtAq8smDnR+jpaZo/zHQ/./server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 5 Apr 2007 19:11:21 -0700 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren(_)delsci.com] Don, It is not exactly what you are looking for, but I just posted a PyMOL animation illustrating the folding of the four-helix bundle protein GCSF. It does a decent job of demonstrating the relationship between primary sequence, 2-D chemical structure, and 3-D tertiary structure (including surface shape). The folding pathway is of course purely illustrative. http://delsci.info/qt QuickTime required (FREE from Apple). Cheers, Warren PS. Kalju -- such beautiful pages! It warms my heart to see PyMOL used in that way :). -- Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice: 1-650-283-6945 Fax: 1-650-989-4082 US Mail: PO Box 1118, Palo Alto, CA 94302-1118, USA > -----Original Message----- > From: owner-chemistry#ccl.net [mailto:owner-chemistry#ccl.net] > Sent: Thursday, April 05, 2007 6:06 PM > To: Warren DeLano > Subject: CCL: Animation of alpha helix wanted > > > Sent to CCL by: Kalju Kahn [kalju(-)chem.ucsb.edu] Dear Donald, > > I do not have a movie of the "folding" but please see if the > few animations or images available at > > http://www.chem.ucsb.edu/~molvisual/prot_struc.html > > meet your need. The animations are in MPG format but > associated scenes can be readily created with PyMOL using the > supplied PDB file and PyMOL script. You can then customize > the visualization toward your on needs. We have also an > animation illustrating the structure of DNA, cooperativity in > hemoglobin, and induced fit in hexokinase. > The whole site is at: > > http://www.chem.ucsb.edu/~molvisual/index.html > > Best wishes, > > Kalju > > ------------------- > > > > Sent to CCL by: "Donald J. Keidel" [keided01**ucr.edu] > > > > I am looking for an animation that someone might have or know > whwere to > > download that shows a protein going from primary structure to > alpha helix. > > I wanted to use it in my course to illustrate how the hydrogen > bonding > > pattern develops. I have searched the net with no luck. Thank > you in > > advance for all suggestions. > > > > Don Keidel> > > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+ > > > > > > > > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Dr. Kalju Kahn > Department of Chemistry and Biochemistry University of > California, Santa Barbara > > > > -= This is automatically added to each message by the mailing > script =- To recover the email address of the author of the > message, please change the strange characters on the top line > to the # sign. You can also look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > >