From owner-chemistry@ccl.net Wed Oct 17 05:34:00 2007 From: "Anouar Benali Anouar.Benali]^[ensiacet.fr" To: CCL Subject: CCL: Hildebrand Parameters Message-Id: <-35394-071017052328-21615-rFRPexv7AytkJeV34UV2SA]_[server.ccl.net> X-Original-From: Anouar Benali Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 17 Oct 2007 11:26:19 +0200 MIME-Version: 1.0 Sent to CCL by: Anouar Benali [Anouar.Benali+/-ensiacet.fr] Hi CCLers, I have a small question... Is it possible, starting from ab initio calculations, to find Hildebrand (Hansen) parameters.. If the answer is yes, then how, and if not, then Why... Thank you very much From owner-chemistry@ccl.net Wed Oct 17 07:15:00 2007 From: "Jens Spanget-Larsen spanget^^^ruc.dk" To: CCL Subject: CCL: Hildebrand Parameters Message-Id: <-35395-071017071421-8590-GgQGGE73fv3xAgOALoDHjA++server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 17 Oct 2007 13:14:07 +0200 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget * ruc.dk] Dear Anouar Benali, I have forwarded you question to Charles M. Hansen himself and he sent me the reply quoted below. You may find more information on his homepage www.hansen-solubility.com where you can read about the second edition of his book. Yours, Jens >--< Charles M. Hansen: "I have calculated Hansen solubility parameters for a lot of lower molecular weight materials, including drugs, plasticizers, solvents, and the like by the methods described in my handbook(s). The second edition (Hansen Solubility Parameters; A User's Handbook, 2nd Ed., CRC Press, Boca Raton FL, 2007) has just come out and the first is now out of print. When sufficiently pressed with only a structure, I estimate the density one way or another, perhaps by comparison with similar materials. The molecular weight divided by the density gives the molar volume that is necessary in the calculations. I then compare structure with what is known for the dispersion parameter. The structures and HSP for 1200 chemicals are given in the second edition of the handbook. The polar and hydrogen bonding parameters can then be estimated by group contributions. I do not use group contributions for the dispersion parameter, since I consider those (even in the handbooks) as inaccurate compared with a simple comparison with what is now considered acceptably close. None of these estimates are completely correct, but I have had surprising success and practically no failures that I know of based on this procedure." ------------------------------------------------------ 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 ------------------------------------------------------ Anouar Benali Anouar.Benali]^[ensiacet.fr wrote: > > Sent to CCL by: Anouar Benali [Anouar.Benali+/-ensiacet.fr] > Hi CCLers, > > I have a small question... Is it possible, starting from ab initio > calculations, to find Hildebrand (Hansen) parameters.. If the answer > is yes, then how, and if not, then Why... > > > Thank you very much > > From owner-chemistry@ccl.net Wed Oct 17 08:43:01 2007 From: "lixian zhang fly_infanta,hotmail.com" To: CCL Subject: CCL: a question about the program to calculate density energyH(r) Message-Id: <-35396-071017063248-14149-DOdPtMNg4UTE9qECz8C22w:server.ccl.net> X-Original-From: "lixian zhang" Date: Wed, 17 Oct 2007 06:32:44 -0400 Sent to CCL by: "lixian zhang" [fly_infanta###hotmail.com] hello, i want to calculate the value of the density energy H(r) and the potential and kinetic energy G(r) and V(r). H(r)=G(r)+V(r). Is there any program to manage it in public domain??? Thanks a lot!! From owner-chemistry@ccl.net Wed Oct 17 09:18:01 2007 From: "Andreas Bick andreas.bick_-_scienomics.com" To: CCL Subject: CCL: Hildebrand Parameters Message-Id: <-35397-071017084040-26762-9zjFkHWnHDCoGJUfCmOMpw*server.ccl.net> X-Original-From: Andreas Bick Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 17 Oct 2007 14:41:36 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Bick [andreas.bick!=!scienomics.com] Dear Anouar, an alternative approach might be atomistic simulations using molecular dynamics, commonly used in polymer simulations. Here you calculate the average energy of your bulk system using a force field, and the sum of the average energies of the individual molecules of your system for a given trajectory. Divide the difference by the cell volume(this gives you the cohesive energy density) and take the square root and you have the solubility parameter. There are software packages around to help you do this, like for example MAPS (http://www.scienomics.com). Best regards Andreas > Sent to CCL by: Jens Spanget-Larsen [spanget * ruc.dk] > Dear Anouar Benali, > I have forwarded you question to Charles M. Hansen himself and he sent > me the reply quoted below. You may find more information on his homepage > > www.hansen-solubility.com > > where you can read about the second edition of his book. > Yours, Jens >--< > > Charles M. Hansen: > > "I have calculated Hansen solubility parameters for a lot of lower > molecular > weight materials, including drugs, plasticizers, solvents, and the > like by > the methods described in my handbook(s). The second edition (Hansen > Solubility Parameters; A User's Handbook, 2nd Ed., CRC Press, Boca > Raton FL, > 2007) has just come out and the first is now out of print. When > sufficiently > pressed with only a structure, I estimate the density one way or another, > perhaps by comparison with similar materials. The molecular weight > divided > by the density gives the molar volume that is necessary in the > calculations. > I then compare structure with what is known for the dispersion parameter. > The structures and HSP for 1200 chemicals are given in the second > edition of > the handbook. The polar and hydrogen bonding parameters can then be > estimated by group contributions. I do not use group contributions for > the > dispersion parameter, since I consider those (even in the handbooks) as > inaccurate compared with a simple comparison with what is now considered > acceptably close. None of these estimates are completely correct, but > I have > had surprising success and practically no failures that I know of > based on > this procedure." > > ------------------------------------------------------ > 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 > ------------------------------------------------------ > > > > Anouar Benali Anouar.Benali]^[ensiacet.fr wrote: > >> >> Sent to CCL by: Anouar Benali [Anouar.Benali+/-ensiacet.fr] >> Hi CCLers, >> >> I have a small question... Is it possible, starting from ab initio >> calculations, to find Hildebrand (Hansen) parameters.. If the answer >> is yes, then how, and if not, then Why... >> >> >> Thank you very muchhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > -- Dr. Andreas Bick Scienomics SARL Sales and Marketing mobile: +491621309945 From owner-chemistry@ccl.net Wed Oct 17 09:53:01 2007 From: "Lixian Zhang fly_infanta{:}hotmail.com" To: CCL Subject: CCL: a question about the program to calculate the density energy H(r) Message-Id: <-35398-071017094725-22174-nDXR3C1IR8e46YpYpRaNqg(~)server.ccl.net> X-Original-From: "Lixian Zhang" Date: Wed, 17 Oct 2007 09:47:22 -0400 Sent to CCL by: "Lixian Zhang" [fly_infanta-*-hotmail.com] hello i want to calculate the value of the desity energy H(r) and the potential and kinetic energy G(r) and V(r) H(r)= G(r)+ V(r) the question is there any program to manage it in public domain???/ thanks a lot!! Lixian Zhang Center for Theoretical Chemistry,Department of Chemistry State Key Laboratory for Physical Chemistry of Solid Surfaces Xiamen University, Xiamen, 361005, China. _______________________________________________ Email:fly_infanta#,#hotmail.com From owner-chemistry@ccl.net Wed Oct 17 10:27:01 2007 From: "soumya s soumya_samineni~!~rediffmail.com" To: CCL Subject: CCL: g98:SCAN Message-Id: <-35399-071017095434-25491-kL9rNYBxAPqsiWoHq2Pxww+/-server.ccl.net> X-Original-From: "soumya s" Date: Wed, 17 Oct 2007 09:54:30 -0400 Sent to CCL by: "soumya s" [soumya_samineni#rediffmail.com] Hi all.. Is it possible to scan, by changing the dihedral angle and optimise the the molecule at each of the dihedral angle (ofcourse keeping the dihedral angle constant for that paricular optimisation)..? thanx in advance soumya From owner-chemistry@ccl.net Wed Oct 17 11:02:00 2007 From: "Andreas Klamt klamt#%#cosmologic.de" To: CCL Subject: CCL: Hildebrand Parameters Message-Id: <-35400-071017105849-21490-dM4iTA5dbqBcVX4wTpkeeQ()server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 17 Oct 2007 16:58:33 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt-,-cosmologic.de] Dear Anaour, basically you can do that with COSMOtherm from COSMOlogic. COSMOtherm calculates the enthalpy of any pure solvent or a mixture starting from DFT/COSMO calculations, and even can split it into electrostatic, vdw, and hb-contributions. From that you can calculate the Hildebrandt/Hansen parameters. COSMOtherm thermodynamic calculations take just a few seconds on top of the DFT/COSMO calculations. But be aware: There are some fudged Hansen parameters in the tables: For example, by definition of the cohesion energy density the hydrogen bond Hansen parameter of acetone must be zero, because acetone has no donors and hence there are no hydrogen bonds in acetone. Nevertheless, the listed hb-Hansen parameter of acetone is greater than zero. This probably has been adjusted by hand in order to express the fact that the solvent acetone very well can interact by hydrogen bonding as an acceptor. Obviously, such empirical fudging will not be reproduced by a systematic calculation of cohesion energy densities. Futhermore, as shown by the work of Mike Abraham and by our sigma moment correlations, the solvent space is approximately 5 dimensional, while the Hansen framework tries to project it to 3 dimensions, with artefacts as shown above. A characterisation of solvents by Abraham parameter coefficients or by our sigma moments (from quantum chemistry) is much more meaningful. But from my long time as comp. chemist in industry I am aware, that there are areas where people just want to know Hansen parameters. For them you can do what I mentioned above. Best regards Andreas Anouar Benali Anouar.Benali]^[ensiacet.fr schrieb: > > Sent to CCL by: Anouar Benali [Anouar.Benali+/-ensiacet.fr] > Hi CCLers, > > I have a small question... Is it possible, starting from ab initio > calculations, to find Hildebrand (Hansen) parameters.. If the answer > is yes, then how, and if not, then Why... > > > Thank you very muchhttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > > > -- ----------------------------------------------------------------------------- Dr. habil. Andreas Klamt COSMOlogic GmbH&CoKG Burscheider Str. 515 51381 Leverkusen, Germany Tel.: +49-2171-73168-1 Fax: +49-2171-73168-9 e-mail: klamt#cosmologic.de web: www.cosmologic.de ----------------------------------------------------------------------------- COSMOlogic Your Competent Partner for Computational Chemistry and Fluid Thermodynamics ----------------------------------------------------------------------------- From owner-chemistry@ccl.net Wed Oct 17 11:42:02 2007 From: "Piotr A. Gauden gaudi..uni.torun.pl" To: CCL Subject: CCL: CCL intermolecular potentials: CCl4, CHCl3, CH2Cl2, CH3Cl, and SF6 Message-Id: <-35401-071017104737-12081-vekjfxZTWTsNR9fAMSQvwg.@.server.ccl.net> X-Original-From: "Piotr A. Gauden" Date: Wed, 17 Oct 2007 10:47:34 -0400 Sent to CCL by: "Piotr A. Gauden" [gaudi()uni.torun.pl] Dear users, We carried computer simulation of CCl4 (CHCl3, CH2Cl2, and CH3Cl) and SF6 and the interactions of the above compounds with the adsorbents possessing and the following surface groups, i.e. -C=O, -COOH, and others. We have just addressed the interaction energy between two carbon tertrachloride or sulfur hexafluoride in which the interaction is due to a dispersion force. We are interested in the relationships with a set of discrete charge is assigned to each above mentioned compounds, similarly as, in the 5-site model by Kollman [Sun, Y.; Spellmeyer, D.; Pearlman, D. A.; Kollman, P. J. Am. Chem Soc. 1992, 114, 6798] for methane molecules. The interaction between a charge on one molecule and a charge on another molecule can be carried out exactly the same way as done with the dispersive interaction sites above. The interaction energy due to electrostatic force between a charge R on a molecule i and a charge on a molecule j is determined via the Coulomb law electrostatic interaction. I would appreciate if anybody could provide me some suggestion on the same. Thanks in advance, Piotr ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ Piotr A. Gauden gaudi!^!uni.torun.pl http://www.chem.uni.torun.pl/~gaudip/wegiel/index.html Uniwersytet Mikolaja Kopernika Nicholas Copernicus University, Katedra Chemii Materiaw, Adsorpcji Chair of Materials Chemistry, i Katalizy Adsorption and Catalysis Zespol Naukowy: Fizykochemia Physicochemistry of Carbon Materialow Weglowych Materials Research Group 87-100 Toru 87-100 Torun ul. Gagarina 7 Gagarin St. 7 Polska Poland Tel. (+48) (056) 611-45-12 Tel. (+48) (056) 611-45-12 Fax. (+48) (056) 654-24-77 Fax. (+48) (056) 654-24-77 ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ From owner-chemistry@ccl.net Wed Oct 17 12:13:00 2007 From: "Eduard Matito ematito{}gmail.com" To: CCL Subject: CCL:G: a question about the program to calculate the density energy H(r) Message-Id: <-35402-071017113329-14361-k2b1GYHLxHmFs3vb0t6ynQ=server.ccl.net> X-Original-From: Eduard Matito Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Wed, 17 Oct 2007 16:33:21 +0200 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Eduard Matito [ematito#gmail.com] The AIMPAC program of Bader and coworkers does such calculations. It works with the wave function files generated by Gaussian or GAMESS and perhaps some other quantum codes. Eduard Eduard Matito Postdoctoral Researcher Lundbeck Foundation, Center for Theoretical Chemistry University of Aarhus, Aarhus (Denmark) http://lctc.dcmedia.dk/index.php?id=69 On Oct 17, 2007, at 3:47 PM, Lixian Zhang fly_infanta{:}hotmail.com wrote: > > Sent to CCL by: "Lixian Zhang" [fly_infanta-*-hotmail.com] > > hello > > i want to calculate the value of the desity energy H(r) and the > potential and kinetic energy G(r) and V(r) > H(r)= G(r)+ V(r) > the question is there any program to manage it in public domain???/ > > thanks a lot!! > > Lixian Zhang > Center for Theoretical Chemistry,Department of Chemistry > State Key Laboratory for Physical Chemistry of Solid Surfaces > Xiamen University, Xiamen, 361005, China. > _______________________________________________ > Email:fly_infanta]^[hotmail.com > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Wed Oct 17 15:36:01 2007 From: "Utpal Sarkar utpalchemiitkgp^^gmail.com" To: CCL Subject: CCL: g98:SCAN Message-Id: <-35403-071017124735-1476-01oVeqSoSNbIAB1nv049yg * server.ccl.net> X-Original-From: "Utpal Sarkar" Content-Type: multipart/alternative; boundary="----=_Part_40108_29893939.1192636272004" Date: Wed, 17 Oct 2007 17:51:11 +0200 MIME-Version: 1.0 Sent to CCL by: "Utpal Sarkar" [utpalchemiitkgp^-^gmail.com] ------=_Part_40108_29893939.1192636272004 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline dear soumya, yes it is possible. what programe you are using? utpal On 10/17/07, soumya s soumya_samineni~!~rediffmail.com < owner-chemistry],[ccl.net> wrote: > > > Sent to CCL by: "soumya s" [soumya_samineni#rediffmail.com] > Hi all.. > Is it possible to scan, by changing the dihedral angle and optimise > the the molecule at each of the dihedral angle (ofcourse keeping the > dihedral angle constant for that paricular optimisation)..? > > thanx in advance > soumya> > > > ------=_Part_40108_29893939.1192636272004 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline dear soumya,
yes it is possible. what programe you are using?
utpal

On 10/17/07, soumya s soumya_samineni~!~rediffmail.com < owner-chemistry],[ccl.net> wrote:

Sent to CCL by: "soumya  s" [soumya_samineni#rediffmail.com]
Hi all..
Is it possible to scan, by changing the dihedral angle and optimise the  the molecule at each of the dihedral angle (ofcourse keeping the dihedral angle constant for that paricular optimisation)..?

thanx in advance
soumya



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------=_Part_40108_29893939.1192636272004-- From owner-chemistry@ccl.net Wed Oct 17 16:19:01 2007 From: "Nick Isachenkov i.nick*|*mail.ru" To: CCL Subject: CCL: GUI for ORCA program Message-Id: <-35404-071017140738-17209-jp64nWZS1c/ro17p/7t/JQ,,server.ccl.net> X-Original-From: "Nick Isachenkov" Date: Wed, 17 Oct 2007 14:07:34 -0400 Sent to CCL by: "Nick Isachenkov" [i.nick()mail.ru] Hi all)). Does anybody know friendly GUI program to visualize some calculation results (i.e. to read *.out files like GaussView does) of ORCA program. By now I know how to view last geometries from Opt procedure (program Molekel) but from *.xyz like files (creates together with *.out), but other information is inaccessible. Any advise will be apperiated))!!! From owner-chemistry@ccl.net Wed Oct 17 16:52:00 2007 From: "Manas Kumar Panda manas..chem.iitb.ac.in" To: CCL Subject: CCL:G: Gaussian 03 optimization failure Message-Id: <-35405-071016120451-18499-qc6mGLtWiVMCN/s3fG5ieA.@.server.ccl.net> X-Original-From: "Manas Kumar Panda" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Tue, 16 Oct 2007 20:03:58 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Manas Kumar Panda" [manas _ chem.iitb.ac.in] Hi all, I am facing a problem during the geometry optimization of a Fe(III)-catechol complex using UB3LYP level, with 6-31G* basis set for C,H,N,O and LANL2DZ for Fe atom. But after certain steps it is showing the following messege and geting error terminated. suggestion please. Scaled steepest descent with Shift=0.050 failed. Search did not lower the energy significantly. Scaled steepest descent with Shift=0.075 failed. Search did not lower the energy significantly. No lower point found -- switch to steepest descent. Search did not lower the energy significantly. No lower point found -- run aborted. Error termination via Lnk1e in /share/apps/g03/l508.exe at Mon Oct 15 22:34:47 2007. Thanks, manas -- Manas Panda Organometallic Synthesis and Homogeneous Catalysis Lab Department of Chemistry IIT Bombay Powai-400076 Contact No. (022)25764129 From owner-chemistry@ccl.net Wed Oct 17 17:34:01 2007 From: "Lorena Romero lorena.webmaster(0)gmail.com" To: CCL Subject: CCL:G: g98:SCAN Message-Id: <-35406-071017131257-12361-IknmhraDRfwvbOmEBWl+qw ~~ server.ccl.net> X-Original-From: "Lorena Romero" Content-Type: multipart/alternative; boundary="----=_Part_35196_11001059.1192634275610" Date: Wed, 17 Oct 2007 11:17:55 -0400 MIME-Version: 1.0 Sent to CCL by: "Lorena Romero" [lorena.webmaster%x%gmail.com] ------=_Part_35196_11001059.1192634275610 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Yes, it is easily done by gaussian. you have to mix to types of keywords, I mean, at the input file you put something like: # *opt=z-matrix* pm3 *nosymm* test (this will perform the optimisation) and when you especify the z matrix you also especify the scan option, in example C C,1,B1 C,2,B2,1,A1 ...... B1=1.52216856 B2=1.51232365 B3=1.51313242 B4=3.97500237 *S 8 -0.2 *(this command will perform the scan, eight steps of -0.2 angstroms) B5=1.36744213 B6=1.41140847 ....... I hope this information can help you. Lorena. (School of Chemistry, Universidad Central de Venezuela). On 17/10/2007, soumya s soumya_samineni~!~rediffmail.com < owner-chemistry!A!ccl.net> wrote: > > > Sent to CCL by: "soumya s" [soumya_samineni#rediffmail.com] > Hi all.. > Is it possible to scan, by changing the dihedral angle and optimise > the the molecule at each of the dihedral angle (ofcourse keeping the > dihedral angle constant for that paricular optimisation)..? > > thanx in advance > soumya -- > "You are a big chemical reaction. Everything you say, all that you do, > all that you see, decide or remember, think or feel is nothing but the > manifestation of the chemical reaction that is you." > > ------=_Part_35196_11001059.1192634275610 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline
Yes, it is easily done by gaussian.
 
you have to mix to types of keywords, I mean, at the input file you put something like:
 
# opt=z-matrix pm3 nosymm test (this will perform the optimisation)
 
and when you especify the z matrix you also especify the scan option, in example
 
 C
 C,1,B1
 C,2,B2,1,A1
 ......
 
 
 B1=1.52216856
 B2=1.51232365
 B3=1.51313242
 B4=3.97500237    S     8     -0.2 (this command will perform the scan, eight steps of -0.2 angstroms)
 B5=1.36744213
 B6=1.41140847
.......
 
I hope this information can help you.
 
Lorena.
(School of Chemistry, Universidad Central de Venezuela).

 
On 17/10/2007, soumya s soumya_samineni~!~rediffmail.com <owner-chemistry!A!ccl.net> wrote:

Sent to CCL by: "soumya  s" [soumya_samineni#rediffmail.com]
Hi all..
Is it possible to scan, by changing the dihedral angle and optimise the  the molecule at each of the dihedral angle (ofcourse keeping the dihedral angle constant for that paricular optimisation)..?

thanx in advance
soumya
 
 
 

--
"You are a big chemical reaction.  Everything you say, all that you do, all that you see, decide or remember, think or feel is nothing but the manifestation of the chemical reaction that is you."

------=_Part_35196_11001059.1192634275610-- From owner-chemistry@ccl.net Wed Oct 17 18:01:01 2007 From: "=?ISO-8859-1?Q?Sina_T=FCreli?= sinatureli:_:gmail.com" To: CCL Subject: CCL: GUI for ORCA program Message-Id: <-35407-071017171005-26436-UNz+KR17sMLIntVQnihedw**server.ccl.net> X-Original-From: "=?ISO-8859-1?Q?Sina_T=FCreli?=" Content-Type: multipart/alternative; boundary="----=_Part_28610_11750796.1192655390089" Date: Thu, 18 Oct 2007 00:09:50 +0300 MIME-Version: 1.0 Sent to CCL by: "=?ISO-8859-1?Q?Sina_T=FCreli?=" [sinatureli|-|gmail.com] ------=_Part_28610_11750796.1192655390089 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline ArgusLab can read from .xyz (if I am not mistaken and that is what you want) files in the format: 140 Mg 14.383900862 27.523036303 35.064958904 C 11.911786481 24.996260203 34.631913004 C 16.735822322 25.162734203 34.075226104 C 16.659093132 30.031398004 34.442794304 . . . where 140 is the number of atoms. Once you have the coordinates and the name of the atoms written in your hand, you can import those to openoffice calculator (opensource form of excel) and divide your results into columns by special paste (maybe microsoft excel can do that too) and then erase the unessary columns containing other charachters and/or numbers, leaving you with only atom names and three coordinates. In short for argus to work the .xyz files you some how have to extract only atom name and coordinates from your results and put the number of atoms at the top. I also reccomend arguslab for CI calculations if you need it. On 10/17/07, Nick Isachenkov i.nick*|*mail.ru wrote: > > > Sent to CCL by: "Nick Isachenkov" [i.nick()mail.ru] > Hi all)). > > Does anybody know friendly GUI program to visualize some calculation > results (i.e. to read *.out files like GaussView does) of ORCA program. By > now I know how to view last geometries from Opt procedure (program Molekel) > but from *.xyz like files (creates together with *.out), but other > information is inaccessible. > > Any advise will be apperiated))!!!> > > > ------=_Part_28610_11750796.1192655390089 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline ArgusLab can read from .xyz (if I am not mistaken and that is what you want) files in the format:

140

Mg    14.383900862    27.523036303    35.064958904
C    11.911786481    24.996260203    34.631913004
C    16.735822322    25.162734203    34.075226104
C    16.659093132    30.031398004    34.442794304
.
.
.

where 140 is the number of atoms. Once you have the coordinates and the name of the atoms written in your hand, you can import those to openoffice calculator (opensource form of excel) and divide your results into columns by special paste (maybe microsoft excel can do that too) and then erase the unessary columns containing other charachters and/or numbers, leaving you with only atom names and three coordinates.

In short for argus to work the .xyz files you some how have to extract only atom name and coordinates from your results and put the number of atoms at the top. I also reccomend arguslab for CI calculations if you need it.

On 10/17/07, Nick Isachenkov i.nick*|*mail.ru <owner-chemistry[]ccl.net> wrote:

Sent to CCL by: "Nick  Isachenkov" [i.nick()mail.ru]
Hi all)).

Does anybody know friendly GUI program to visualize some calculation results (i.e. to read *.out files like GaussView does) of ORCA program. By now I know how to view last geometries from Opt procedure (program Molekel) but from *.xyz like files (creates together with *.out), but other information is inaccessible.

Any advise will be apperiated))!!!



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------=_Part_28610_11750796.1192655390089-- From owner-chemistry@ccl.net Wed Oct 17 20:40:01 2007 From: "William F. Polik polik{=}hope.edu" To: CCL Subject: CCL:G: g98:SCAN Message-Id: <-35408-071017203804-6326-4s151BQXxUrvrjgJG9iAzw-#-server.ccl.net> X-Original-From: "William F. Polik" Date: Wed, 17 Oct 2007 20:38:00 -0400 Sent to CCL by: "William F. Polik" [polik . hope.edu] A great way to learn how to construct input files for a variety of programs (gaussian, gamess, mopac, molpro, q-chem, nwchem) and jobs (energy, geometry optimization, frequency, coordinate scan, etc.) is to use the WebMO Working Demo: www.webmo.net/demo After logging in (username = guest and password = guest), choose new job, build your molecule using the 3-D editor, select the computational engine, and select the desired job type. Before submitting the job, select the Preview tab and click Generate. The output file that would be submitted to the server is displayed in a textbox. For example, an optimized scan of the ethane dihedral angle produces: N HF/3-21G OPT=AddRedundant NOSYMMETRY C2H6 0 1 H C 1 B1 C 2 B2 1 A1 H 3 B3 2 A2 1 D1 H 2 B4 1 A3 3 D2 H 2 B5 1 A4 3 D3 H 3 B6 2 A5 4 D4 H 3 B7 2 A6 4 D5 A5 110.99449 A6 110.99154 B1 1.1147184 B2 1.5315728 B3 1.1147166 B4 1.1147166 B5 1.1147169 B6 1.1147101 B7 1.1147218 D1 -180.00000 D2 -121.82588 A1 110.98986 D3 121.80696 A2 110.98699 D4 119.99922 A3 107.91146 A4 107.90946 D5 -119.99861 4 3 2 1 -180.00000 S 36 10.00 This can serve as a template for your own jobs. Will Polik At 09:54 AM 10/17/2007, you wrote: >Sent to CCL by: "soumya s" [soumya_saminenirediffmail.com] >Hi all.. >Is it possible to scan, by changing the dihedral angle and optimise the >the molecule at each of the dihedral angle (ofcourse keeping the dihedral >angle constant for that paricular optimisation)..? > >thanx in advance >soumya ================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik{}hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================ From owner-chemistry@ccl.net Wed Oct 17 21:46:01 2007 From: "William F. Polik polik##hope.edu" To: CCL Subject: CCL:G: g98:SCAN Message-Id: <-35409-071017211852-26262-UGblJhHCRhLlm/aY0tUb9g(!)server.ccl.net> X-Original-From: "William F. Polik" Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Wed, 17 Oct 2007 20:15:55 -0400 Mime-Version: 1.0 Sent to CCL by: "William F. Polik" [polik-.-hope.edu] A great way to learn how to construct input files for a variety of programs (gaussian, gamess, mopac, molpro, q-chem, nwchem) and jobs (energy, geometry optimization, frequency, coordinate scan, etc.) is to use the WebMO Working Demo: www.webmo.net/demo After logging in (username = guest and password = guest), choose new job, build your molecule using the 3-D editor, select the computational engine, and select the desired job type. Before submitting the job, select the Preview tab and click Generate. The output file that would be submitted to the server is displayed in a textbox. For example, an optimized scan of the ethane dihedral angle produces: >#N HF/3-21G OPT=AddRedundant NOSYMMETRY > >C2H6 > >0 1 >H >C 1 B1 >C 2 B2 1 A1 >H 3 B3 2 A2 1 D1 >H 2 B4 1 A3 3 D2 >H 2 B5 1 A4 3 D3 >H 3 B6 2 A5 4 D4 >H 3 B7 2 A6 4 D5 > >A5 110.99449 >A6 110.99154 >B1 1.1147184 >B2 1.5315728 >B3 1.1147166 >B4 1.1147166 >B5 1.1147169 >B6 1.1147101 >B7 1.1147218 >D1 -180.00000 >D2 -121.82588 >A1 110.98986 >D3 121.80696 >A2 110.98699 >D4 119.99922 >A3 107.91146 >A4 107.90946 >D5 -119.99861 > >4 3 2 1 -180.00000 S 36 10.00 This can serve as a template for your own jobs. Will Polik At 09:54 AM 10/17/2007, you wrote: >Sent to CCL by: "soumya s" [soumya_samineni#rediffmail.com] >Hi all.. >Is it possible to scan, by changing the dihedral angle and optimise >the the molecule at each of the dihedral angle (ofcourse keeping >the dihedral angle constant for that paricular optimisation)..? > >thanx in advance >soumya================================ Dr. William F. Polik Hofma Professor of Chemistry Department of Chemistry Hope College 35 East 12th Street Holland, MI 49422-9000 USA polik#%#hope.edu http://www.chem.hope.edu/~polik tel: (616) 395-7639 fax: (616) 395-7118 ================================