From owner-chemistry@ccl.net Thu Sep 30 02:52:00 2010 From: "Daniel Jana dfjana]|[gmail.com" To: CCL Subject: CCL: Help needed Message-Id: <-42865-100930024854-13052-mpnnPQq8pbjI8iPlhYI9kA(_)server.ccl.net> X-Original-From: Daniel Jana Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Sep 2010 08:48:42 +0200 MIME-Version: 1.0 Sent to CCL by: Daniel Jana [dfjana_-_gmail.com] Hello, Why not going the extra step and trying out Linux? It may be a bit of a problematic approach at first, having to learn a new operating system, but in the end there are many extra-features that may help. To start, plenty of things can be done with simple shell scripts without having to resort to more "appropriate" programming languages (C, Fortran, ...). Fortran itself is either installed by default or easily installable with one or two commands in most distributions. There are plenty of editors for Linux (and for Windows) that can do that job, many of them capable of syntax highlighting which helps a lot (instead of having all code in black it colors functions, logical statements and so on). Since going straight to your answer would be too easy, let's see a couple of points before: 1) That subject... Everyone making a post in CCL needs help (unless you are replying to a post). So, putting on the subject "Help needed" is not very explanatory. In fact, we all know you need help already, that's why the email is here. Not only that subject is not very... helpful (pun intended), but it is even disrespectful as it seems to indicate we should urge to solve your problem, like our lives are less important than yours (a free tip, they may be for you, but that is not general). Write a subject that indicates what the problem is, so that people who actually understand about the topic can assist you. You will see you even benefit from this (I tend not to read these "Please help" emails, for instance). 2) Please take the time to search on your favorite search engine about the subject you are interested in before posting something here. Have you even tried "Fortran XP" in Google, for instance? At least if you do, you can come and make a somehow more informed question, something like "I found both G95 and MinGW for Windows, can anyone comment on performance, features and bugs of each? Which one is best overall?" At least that way the answer won't be a simple "Here's the google result page for that" and actual knowledge is passed on to you and to the list. Now, to (finally) answer your question: I never used Windows for this kind of stuff, but this project seems ok: http://mingw.org/ It has both C and Fortran compilers so it should help with all the needs you have. As for editors, I don't know any for windows (any decent ones, that is. Notepad gets the job done). I googled for "syntax highlighting windows" and one free program called Notepad++ came up first. Maybe that's a good option. Best regards, Daniel PS - Another rule of netiquette is "keep the email short". I still haven't managed to learn (or apply) this one. On 30 September 2010 04:23, rocky walden rocky.walden19(!)gmail.com wrote: > Hi All, >    I am planning to learn FORTRAN language, and i need where can i download > the editors to write the code and compile it. >    Can any one send me a link where i can download Fortran 77/90/95 for > windows XP. > > > Regards > Walden > From owner-chemistry@ccl.net Thu Sep 30 04:27:01 2010 From: "Thomas Gkourmpis thomas.gkourmpis|,|borealisgroup.com" To: CCL Subject: CCL:G: Problem with Frequency Calculations in a Solvent Message-Id: <-42866-100930042556-446-mIkSbS9TapCqFKO7VatWDA~!~server.ccl.net> X-Original-From: "Thomas Gkourmpis" Date: Thu, 30 Sep 2010 04:25:55 -0400 Sent to CCL by: "Thomas Gkourmpis" [thomas.gkourmpis,borealisgroup.com] Hello everyone I've been searching through the forum for a while trying to get some answers to my problem but so far I got confused, so I thought of actually asking all of you for your opinions. I am trying to perform a geometry optimisation followed by a frequency calculation on a molecule (let's say tertbutoxy radical or methane) in the presence of heptane using Gaussian09W. According to the Gaussian Manual one cannot perform opt freq calculations in one step, so I do the geometry optimisation first followed by the frequency calculation (by reading from the previous checkpoint file). The input parameters I am using are: Optimisation %nprocshared=4 %chk=C:\Software\G09W\Projects\Tertbutoxy Radical with Solvent opt.chk #p opt ub3lyp/6-311g(d,p) scrf=(solvent=heptane,read) nosymm geom=connectivity 0 2 ... OFac=0.8 RMin=0.5 nosymmcav Radii=Pauling GeomView Frequency %nprocshared=4 %chk=C:\Software\G09W\Projects\Tertbutoxy Radical with Solvent freq.chk #p freq=noraman ub3lyp/6-311g(d,p) scrf=(solvent=heptane,read) nosymm guess=read geom=connectivity 0 2 ... OFac=0.8 RMin=0.5 nosymmcav Radii=Pauling GeomView My optimisation finishes without any issues but when I run the frequency calculation I get a lot of imaginary frequencies that I don't know how to correct for. The output of the frequency caclulation is Dipole =-1.16779194D-01-9.65682598D-06 9.29953865D-01 Polarizability= 5.51891627D+01-2.05786740D-02 3.27901680D+02 -8.98045149D-01-1.98610807D-03 5.45659145D+01 Full mass-weighted force constant matrix: Low frequencies ----4971.1317 -398.9066 -361.3915 -350.1968 -122.9239 -67.5265 Low frequencies --- -44.5338 -0.0011 -0.0010 ****** 4 imaginary frequencies (negative Signs) ****** Diagonal vibrational polarizability: 2.4992807 285.7442495 1.4566692 Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), depolarization ratios for plane and unpolarized incident light, reduced masses (AMU), force constants (mDyne/A), and normal coordinates: 1 2 3 A A A Frequencies -- -4971.1297 -396.3722 -347.3026 Red. masses -- 3.1724 1.0121 1.0363 Frc consts -- 46.1894 0.0937 0.0736 IR Inten --255900.9075 0.0000 0.0023 This type of result (all frequencies negative) is present in every frequency calculation I am doing in a solvent, which tells me that it is not a freak optimisation but something consistent. Any ideas what I am doing wrong? If you have any suggestions on the strategy on how to obtain reliable gibbs free energies for my molecules in solvent I am more than happy to listen and try them out. I don't really have a lot of experience in QM calculations so if I am doing something stupid please do not hesitate to let me know. Thanks a lot in advance Thomas From owner-chemistry@ccl.net Thu Sep 30 07:44:01 2010 From: "Vincent Leroux vincent.leroux_+_loria.fr" To: CCL Subject: CCL: selecting compounds for protein co-crystallization Message-Id: <-42867-100930031810-3295-phqL67u6Z5Jz/Q2lhyscVQ]-[server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Sep 2010 09:18:00 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux**loria.fr] Hi, This is a *computational* chemistry list here, so this may not be the best place to ask! In short: you add those compounds to stabilize your protein, so it crystallizes better. If you have a known ligand for your protein, it might do wonders but will probably change your protein conformational state around the active site, which you might or might not want to see. How to choose those compounds, etc.: this is all the crystallographers' expertise! Ask them. Do not be surprised if for your system, each crystallographer gives you a different suggestion. If protein crystallization was be an experimental process so simple there exists generic, reliable "recipes" to perform it, we would know ;-) Regards, VL Le 30/09/10 02:29, Qi Chen qchen,,lilly.com a écrit : > > Sent to CCL by: "Qi Chen" [qchen\a/lilly.com] > I am looking for information on what kinds of factors one should consider when selecting compounds for protein co-crystallization in general, and why. Thanks! > > > From owner-chemistry@ccl.net Thu Sep 30 08:19:00 2010 From: "Vincent Leroux vincent.leroux * loria.fr" To: CCL Subject: CCL: Help needed Message-Id: <-42868-100930030056-16688-eKs0HrPPeKh2L1eJ1ZBKBA-*-server.ccl.net> X-Original-From: Vincent Leroux Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Sep 2010 09:00:38 +0200 MIME-Version: 1.0 Sent to CCL by: Vincent Leroux [vincent.leroux#%#loria.fr] Hi Rocky, There exist old G77 versions compiled for Windows if you search well. But those are quite obsolete and require to use the DOS terminal which is a joke compared to Unix Shells. Good Fortran 90/95 compilers for Windows like the Intel one are all commercial. You really need to get and install a Linux system if you plan to do scientific programming seriously. Here is your link: www.ubuntu.com All you have to do after installation is to open a terminal and type: sudo apt-get install gfortran emacs and accept the dependencies. You should also know that Fortran code is better interfaced with a higher level language, especially for everything that relates to user interaction - learning Python is a good idea. In advance: please do not ask questions about Linux, how to use it etc. on a computer chemistry mailing list. The Linux communities are huge and very friendly to beginners, and the Ubuntu system really is made so that even children can use it quickly. I am also wondering: do you have some kind of advisor? Asking such simple questions like "Where can I download Fortran for Windows" is really a sign either your advisor is incompetent, or that you fail to understand that this is his role to help you with such inquiries, not that of a specialized mailing list. Regards VL Le 30/09/10 04:49, rocky walden rocky.walden19(!)gmail.com a écrit : > Hi All, > I am planning to learn FORTRAN language, and i need where can i > download the editors to write the code and compile it. > Can any one send me a link where i can download Fortran 77/90/95 for > windows XP. > > > Regards > Walden From owner-chemistry@ccl.net Thu Sep 30 08:54:00 2010 From: "Simon Halstead joyjoyhappyjoy[a]yahoo.co.uk" To: CCL Subject: CCL: Help needed Message-Id: <-42869-100930041658-22126-8A7PWutEn+Q9E29Nn4SLQw : server.ccl.net> X-Original-From: Simon Halstead Content-Type: text/plain; charset=us-ascii Date: Thu, 30 Sep 2010 08:16:49 +0000 (GMT) MIME-Version: 1.0 Sent to CCL by: Simon Halstead [joyjoyhappyjoy()yahoo.co.uk] On my windows PC, I tend to use cygwin, which is basically a Linux interface for use with windows, to compile and run programs. To write/edit code, I use Photran (a modified version of eclipse) which has the syntax highlighting as mentioned by Daniel. http://www.cygwin.com/ http://www.eclipse.org/photran/ Also, as Daniel mentioned, please try to look a little first - these things are pretty easy to find. ----- Original Message ---- > From: Daniel Jana dfjana]|[gmail.com To: "Halstead, Simon " Sent: Thu, September 30, 2010 2:48:42 PM Subject: CCL: Help needed Sent to CCL by: Daniel Jana [dfjana_-_gmail.com] Hello, Why not going the extra step and trying out Linux? It may be a bit of a problematic approach at first, having to learn a new operating system, but in the end there are many extra-features that may help. To start, plenty of things can be done with simple shell scripts without having to resort to more "appropriate" programming languages (C, Fortran, ...). Fortran itself is either installed by default or easily installable with one or two commands in most distributions. There are plenty of editors for Linux (and for Windows) that can do that job, many of them capable of syntax highlighting which helps a lot (instead of having all code in black it colors functions, logical statements and so on). Since going straight to your answer would be too easy, let's see a couple of points before: 1) That subject... Everyone making a post in CCL needs help (unless you are replying to a post). So, putting on the subject "Help needed" is not very explanatory. In fact, we all know you need help already, that's why the email is here. Not only that subject is not very... helpful (pun intended), but it is even disrespectful as it seems to indicate we should urge to solve your problem, like our lives are less important than yours (a free tip, they may be for you, but that is not general). Write a subject that indicates what the problem is, so that people who actually understand about the topic can assist you. You will see you even benefit from this (I tend not to read these "Please help" emails, for instance). 2) Please take the time to search on your favorite search engine about the subject you are interested in before posting something here. Have you even tried "Fortran XP" in Google, for instance? At least if you do, you can come and make a somehow more informed question, something like "I found both G95 and MinGW for Windows, can anyone comment on performance, features and bugs of each? Which one is best overall?" At least that way the answer won't be a simple "Here's the google result page for that" and actual knowledge is passed on to you and to the list. Now, to (finally) answer your question: I never used Windows for this kind of stuff, but this project seems ok: http://mingw.org/ It has both C and Fortran compilers so it should help with all the needs you have. As for editors, I don't know any for windows (any decent ones, that is. Notepad gets the job done). I googled for "syntax highlighting windows" and one free program called Notepad++ came up first. Maybe that's a good option. Best regards, Daniel PS - Another rule of netiquette is "keep the email short". I still haven't managed to learn (or apply) this one. On 30 September 2010 04:23, rocky walden rocky.walden19(!)gmail.com wrote: > Hi All, > I am planning to learn FORTRAN language, and i need where can i download > the editors to write the code and compile it. > Can any one send me a link where i can download Fortran 77/90/95 for > windows XP. > > > Regards > Waldenhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Thu Sep 30 09:28:00 2010 From: "Massimiliano Porrini mozz76**gmail.com" To: CCL Subject: CCL: helical content time series Message-Id: <-42870-100930081306-28209-vDpx8FKaL3zOS5txcu0HxQ!^!server.ccl.net> X-Original-From: Massimiliano Porrini Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252 Date: Thu, 30 Sep 2010 13:12:58 +0100 MIME-Version: 1.0 Sent to CCL by: Massimiliano Porrini [mozz76]-[gmail.com] Dear Xevi, Cesar, Case and CCL community, Firstly I would like to thank you for your hints. Then I wish to point out that I knew that there are several tools (even with Amber) to assign the secondary structure to every single residues, in according to the DSSP. But what I would like to work out is the time series of the so called "helical content", that is an overall description of the helical content (indeed) evolution of the whole structure (in my case a peptide). To better understand I am speaking about the q(t) calculated in the following paper: Nymeyer, H.; Gnanakaran, S.; García, A.E. Atomic simulations of protein folding using the replica exchange algorithm. Meth. Enzymol., 2004, 383, 119–149. I am going to have a look at Simulaid though, as one of the things it performs is called: "Variety of helix analyses (TRAJELIX)" Many thanks again, Massimiliano -- Dr. Massimiliano Porrini Dr. P. E. Barran Research Group University of Edinburgh School of Chemistry Joseph Black Building West Mains Road Edinburgh, EH9 3JJ Tel: +44 (0) 131 650 7748 Fax: +44 (0) 131 650 6453 E-mail : mozz76]^[gmail.com or maxp]^[iesl.forth.gr From owner-chemistry@ccl.net Thu Sep 30 10:03:00 2010 From: "Phil Hasnip pjh503-*-york.ac.uk" To: CCL Subject: CCL: Help needed Message-Id: <-42871-100930084408-26297-vLTdYrR+gURSBNfHUFnERg^-^server.ccl.net> X-Original-From: Phil Hasnip Content-Type: text/plain; format=flowed; charset=ISO-8859-1 Date: 30 Sep 2010 13:43:57 +0100 Mime-Version: 1.0 Sent to CCL by: Phil Hasnip [pjh503(-)york.ac.uk] Dear Walden, I know you've already had several useful replies, but just to add one thing to them -- if you don't want to install linux itself you could try Cygwin/X, which gives you a free linux-like environment but runs under Windows. You can get many linux tools for free (including the Fortran compiler "gfortran", and many editors). Yours, Phil Hasnip ------------------------------------------------------- Dr Phil Hasnip Email: pjh503*york.ac.uk Dept of Physics University of York Tel: +44 (0)1904 434624 York YO10 5DD From owner-chemistry@ccl.net Thu Sep 30 13:35:01 2010 From: "Kalju Kahn kalju!=!chem.ucsb.edu" To: CCL Subject: CCL: Help needed (learning Fortran) Message-Id: <-42872-100930002546-19323-/lRSjRLr/s3K/04lgiS3Hg[]server.ccl.net> X-Original-From: "Kalju Kahn" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 29 Sep 2010 21:25:37 -0700 MIME-Version: 1.0 Sent to CCL by: "Kalju Kahn" [kalju]~[chem.ucsb.edu] Walden, One way to start if you insist on learning it under Windows is too get MinGW, then head to http://www.g95.org/ and grab G95. For editors, any text editor with a decent color-coding will do. Bluefish under MinGW is one good option. For easy learning, consider starting coding in F, before moving up to full Fortran 95. You also need to ask yourself if you really need to know Fortran 77 (e.g. you will be in a team managing a legacy program), or will the knowledge of more modern versions be sufficient (e.g. you want to write your own code that does not borrow bits from other programs). Good luck, Kalju > Hi All, > I am planning to learn FORTRAN language, and i need where can i > download > the editors to write the code and compile it. > Can any one send me a link where i can download Fortran 77/90/95 for > windows XP. > > > Regards > Walden > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dr. Kalju Kahn Department of Chemistry and Biochemistry UC Santa Barbara, CA 93106 From owner-chemistry@ccl.net Thu Sep 30 14:38:01 2010 From: "Eike Huebner mail-#-eike-huebner.de" To: CCL Subject: CCL: Help needed Message-Id: <-42873-100930091500-25389-rH6Mvcxb9vDNqqjUZsLyGg]-[server.ccl.net> X-Original-From: "Eike Huebner" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="ISO-8859-1" Date: Thu, 30 Sep 2010 15:14:04 +0200 Mime-Version: 1.0 Sent to CCL by: "Eike Huebner" [mail:eike-huebner.de] Hi, Take a look at the windows binaries of the gnu Fortran compiler (gfortran) http://gcc.gnu.org/wiki/GFortranBinariesWindows http://gcc.gnu.org/wiki/GFortranBinaries#Windows direkt Download for XP: http://users.humboldt.edu/finneyb/gfortran-windows.exe The compiler is Fortran 95 compatible and all common optimization flags are recognized, too. Installation ist rather simple (Installer) and the compiler is called from the command prompt (gfortran). Any text editor to write the code will do, just save as .f., although some editors are known which may help by syntax highlighting. General Fortran code is not system-specific for windows/linux so you will find programs compile easily on linux and windows systems with the gfortran compiler, performance is more or less the same. Especially to hand small tools to Windows users we found the compiler very helpful. Things change of course for highly optimized and more complex program environments. Regards, Eike Hübner >Le 30/09/10 04:49, rocky walden rocky.walden19(!)gmail.com a écrit : >> Hi All, >> I am planning to learn FORTRAN language, and i need where can i >> download the editors to write the code and compile it. >> Can any one send me a link where i can download Fortran 77/90/95 for >> windows XP. >> >> >> Regards >> Walden > From owner-chemistry@ccl.net Thu Sep 30 18:25:00 2010 From: "Jamin Krinsky jamink_._berkeley.edu" To: CCL Subject: CCL: Difference between IRC and minimization from TS Message-Id: <-42874-100930182122-24007-mKI274xTM/GlE+JF9f3mZA]~[server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Sep 2010 15:21:13 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink() berkeley.edu] Hi Jan, A minimization generally does not actually follow any kind of physically relevant trajectory, so simply minimizing on both sides of the transition state does not PROVE that that TS (and the associated trajectory) connects the reactant and product. It very often turns out to be the case but if you want to be rigorous you've got to do the IRC. Best regards, Jamin On Tue, Sep 28, 2010 at 6:45 AM, Jan Dillen jlmd|-|sun.ac.za wrote: > > Sent to CCL by: "Jan  Dillen" [jlmd-$-sun.ac.za] > Could anyone explain whether there is a practical (in terms of results)difference in doing an IRC (in Cartesian coordinates) to find the two minima downhill from a transition state on the one hand, and doing a minimization of two structures that were distorted in opposite directions from the same TS using the eigenvector associated with the negative frequency on the other. I am not interested in the actual trajectory, only in establishing whether the TS is the correct one between the two minima. > > Jan>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Sep 30 18:59:00 2010 From: "Jamin Krinsky jamink|-|berkeley.edu" To: CCL Subject: CCL:G: Problem with Frequency Calculations in a Solvent Message-Id: <-42875-100930183310-13852-8CX0RGQvf8cy6p3//4wn+w(~)server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 30 Sep 2010 15:33:02 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink/a\berkeley.edu] Hi Thomas, Not to be demeaning but you said you're relatively new to this so I have to ask, are you sure that the structure you are using for the frequency calculation is the LAST structure from the optimization? GaussView might screw up and give you the first if you don't watch out. In the linux versions of Gaussian you most certainly CAN to opt and freq in the same job, just specify "opt freq=noraman" in the route section. Assuming you still have the problem after checking the above I'd start troubleshooting by taking the "read" out of the scrf section (and also deleting the extra input for that) and see if something you specified for the solvent correction is messing with things. Jamin On Thu, Sep 30, 2010 at 1:25 AM, Thomas Gkourmpis thomas.gkourmpis|,|borealisgroup.com wrote: > > Sent to CCL by: "Thomas  Gkourmpis" [thomas.gkourmpis,borealisgroup.com] > Hello everyone > > I've been searching through the forum for a while trying to get some answers to my problem but so far I got confused, so I thought of actually asking all of you for your opinions. > > I am trying to perform a geometry optimisation followed by a frequency calculation on a molecule (let's say tertbutoxy radical or methane) in the presence of heptane using Gaussian09W. > > According to the Gaussian Manual one cannot perform opt freq calculations in one step, so I do the geometry optimisation first followed by the frequency calculation (by reading from the previous checkpoint file). > > The input parameters I am using are: > > Optimisation > > %nprocshared=4 > %chk=C:\Software\G09W\Projects\Tertbutoxy Radical with Solvent opt.chk > #p opt ub3lyp/6-311g(d,p) scrf=(solvent=heptane,read) nosymm geom=connectivity > > 0 2 > > ... > > OFac=0.8 > RMin=0.5 > nosymmcav > Radii=Pauling > GeomView > > Frequency > > %nprocshared=4 > %chk=C:\Software\G09W\Projects\Tertbutoxy Radical with Solvent freq.chk > #p freq=noraman ub3lyp/6-311g(d,p) scrf=(solvent=heptane,read) nosymm > guess=read geom=connectivity > > 0 2 > > ... > > OFac=0.8 > RMin=0.5 > nosymmcav > Radii=Pauling > GeomView > > My optimisation finishes without any issues but when I run the frequency calculation I get a lot of imaginary frequencies that I don't know how to correct for. The output of the frequency caclulation is > >  Dipole        =-1.16779194D-01-9.65682598D-06 9.29953865D-01 >  Polarizability= 5.51891627D+01-2.05786740D-02 3.27901680D+02 >                -8.98045149D-01-1.98610807D-03 5.45659145D+01 >  Full mass-weighted force constant matrix: >  Low frequencies ----4971.1317 -398.9066 -361.3915 -350.1968 -122.9239  -67.5265 >  Low frequencies ---  -44.5338   -0.0011   -0.0010 >  ******    4 imaginary frequencies (negative Signs) ****** >  Diagonal vibrational polarizability: >        2.4992807     285.7442495       1.4566692 >  Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering >  activities (A**4/AMU), depolarization ratios for plane and unpolarized >  incident light, reduced masses (AMU), force constants (mDyne/A), >  and normal coordinates: >                     1                      2                      3 >                     A                      A                      A >  Frequencies -- -4971.1297              -396.3722              -347.3026 >  Red. masses --     3.1724                 1.0121                 1.0363 >  Frc consts  --    46.1894                 0.0937                 0.0736 >  IR Inten    --255900.9075                 0.0000                 0.0023 > > This type of result (all frequencies negative) is present in every frequency calculation I am doing in a solvent, which tells me that it is not a freak optimisation but something consistent. Any ideas what I am doing wrong? > > If you have any suggestions on the strategy on how to obtain reliable gibbs free energies for my molecules in solvent I am more than happy to listen and try them out. > > I don't really have a lot of experience in QM calculations so if I am doing something stupid please do not hesitate to let me know. > > Thanks a lot in advance > > Thomas>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Thu Sep 30 21:47:01 2010 From: "Alex M Clark aclark.xyz|a|gmail.com" To: CCL Subject: CCL: Mobile Molecular DataSheet v1.1 released Message-Id: <-42876-100930205024-13364-sF/Z4oayBIqknzUNeK1vzg#server.ccl.net> X-Original-From: "Alex M Clark" Date: Thu, 30 Sep 2010 20:50:23 -0400 Sent to CCL by: "Alex M Clark" [aclark.xyz%gmail.com] Molecular Materials Informatics has recently released version 1.1 of the Mobile Molecular DataSheet (MMDS) for BlackBerry and iPhone/iPod/iPad devices, which are available on their respective company stores: http://appworld.blackberry.com/webstore/content/10662 http://itunes.apple.com/ca/app/mobile-molecular-datasheet/id383661863?mt=8 Apart from a laundry list of minor improvements, the main feature that has been added to both platforms is a webservices client. This enables remote functionality to be executed from the mobile device. The input requirements are specified by the service itself, and consist of a set of fields containing molecular structures, datasheets, text, numbers, option lists, flags, etc. The user fills out the fields and submits the request, and the service returns a new datasheet with relevant content. Two webservices are currently hosted by MMI, which provide bridges to the PubChem and ChEBI online databases. Structure searches can be performed by using the MMDS webservices client on a mobile device: http://molmatinf.com/srchpubchem.html http://molmatinf.com/srchchebi.html The protocol used for MMDS webservices is a simple XML dialect, and is fully documented. A new service can be implemented using several pages of PHP, and sample code is provided: http://molmatinf.com/websvcproto.html http://molmatinf.com/websvcexample.html All comments and inquiries are welcome. Best regards, Alex Clark President, Molecular Materials Informatics http://molmatinf.com aclark(_)molmatinf.com