From owner-chemistry@ccl.net Tue Jul 31 02:12:00 2007 From: "Tamas Gunda tgunda2**puma.unideb.hu" To: CCL Subject: CCL:G: Optimized molecules - Draw Message-Id: <-34832-070730091505-6688-pzYVOMTxrbtVkkD1ukl2+g a server.ccl.net> X-Original-From: "Tamas Gunda" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0021_01C7D2B3.4E002600" Date: Mon, 30 Jul 2007 14:09:55 +0200 MIME-Version: 1.0 Sent to CCL by: "Tamas Gunda" [tgunda2=puma.unideb.hu] This is a multi-part message in MIME format. ------=_NextPart_000_0021_01C7D2B3.4E002600 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Re: CCL:G: Optimized molecules - DrawMost crystallographic programs can = create that type of graphical output.=20 Tamas E. Gunda ----- Original Message -----=20 From: Fco. Javier Modrego modrego{:}unizar.es=20 To: Gunda, Tamas E =20 Sent: Monday, July 30, 2007 11:12 Subject: CCL:G: Optimized molecules - Draw They seem very similar to those on http://www.ccc.uga.edu/~swheele2/hfsmol/ but I dont think the program is publicly available... F.J. Modrego can you people tell me which software has been used to draw the = following molecule click on link below http://img2.freeimagehosting.net/image.php?89ebec4e78.jpg also can someone recommend me a software that can make colorless, = editable and publishable drawing of optimized geometry a molecule = generated by Gaussview/Gaussian 03 -------------------------------------------------------------------------= --- Ready for the edge of your seat? Check out tonight's top picks on = Yahoo! TV. --=20 Dr. F.J. Modrego Department of Inorganic Chemistry Facultad de Ciencias University of Zaragoza 50009 ZARAGOZA SPAIN Tel <34>-976-762288 Fax <34>-976-761187 E-mail: modrego-*-unizar.es ------=_NextPart_000_0021_01C7D2B3.4E002600 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Re: CCL:G: Optimized molecules - Draw
Most crystallographic programs = can create that=20 type of graphical output.
 
Tamas E. Gunda
 
----- Original Message -----
From:=20 Fco.=20 Javier Modrego modrego{:}unizar.es
To: Gunda, Tamas E =
Sent: Monday, July 30, 2007 = 11:12
Subject: CCL:G: Optimized = molecules -=20 Draw

They seem very similar to those on
http://www.ccc.uga.edu/= ~swheele2/hfsmol/
but I dont think the program is publicly available...

       =20         F.J. = Modrego




can you people tell me which = software=20 has been used to draw the following molecule

click on link=20 below

http:/= /img2.freeimagehosting.net/image.php?89ebec4e78.jpg

also=20 can someone recommend me a software that can make colorless, = editable and=20 publishable drawing of optimized geometry a molecule generated by=20 Gaussview/Gaussian 03
 
Ready for the edge of your seat? = Check = out=20 tonight's top picks on Yahoo! TV.


--=20
 Dr. F.J. Modrego
 Department of Inorganic=20 Chemistry
 Facultad de Ciencias
 University of=20 Zaragoza
 50009 ZARAGOZA
 SPAIN
 Tel=20 <34>-976-762288
 Fax=20 <34>-976-761187
 E-mail: =20 modrego-*-unizar.es
------=_NextPart_000_0021_01C7D2B3.4E002600-- From owner-chemistry@ccl.net Tue Jul 31 08:08:01 2007 From: "Michael Shokhen shokhen]=[mail.biu.ac.il" To: CCL Subject: CCL: software for equipotential lines ? Message-Id: <-34833-070731075054-21796-mQgbazzxsHxkiqSAsLLzkw . server.ccl.net> X-Original-From: "Michael Shokhen" Date: Tue, 31 Jul 2007 07:50:50 -0400 Sent to CCL by: "Michael Shokhen" [shokhen]=[mail.biu.ac.il] Dear CCL Subscribers, I would appreciate if somebody can address me to a graphical software (for Windows) for equipotential lines building ( presentation of 2D potential surface, E(x,y)). The feature of my data points, E(x,y), is that X and Y coordinates are chaotically distributed over the (X,Y) plane, so E(x,y) cannot be organized in a regular rectangular grid (table with rows and columns enumerated according to fixed X and Y values, so Excel graphical tools are usless here. Thank you, Michael From owner-chemistry@ccl.net Tue Jul 31 09:17:00 2007 From: "Gonzalo Jim nez-Os s gonzalo.jimenez]![unirioja.es" To: CCL Subject: CCL:G: "gen" keyword for ONIOM Message-Id: <-34834-070731060848-5225-11sWUjOLKIwfb47/2t4nGQ*server.ccl.net> X-Original-From: "Gonzalo Jim nez-Os s" Date: Tue, 31 Jul 2007 06:08:44 -0400 Sent to CCL by: "Gonzalo Jim nez-Os s" [gonzalo.jimenez-x-unirioja.es] Dear Nihan, I frequently get similar messages using ONIOM in G03, but I think that it is not striclty related to the use of the "gen" keyword. Note that employing the AM1 method generates a lot of warnings, what is a bit disturbing...Nevertheless, the failure in the SCF step (over 129 cycles) is more related with some inconsistency within the QM part. Try to add the keyword "geom=connectivity" to the input and/or to prepare a better starting structure in order to facilitate the generation of a more realiable initial guess. I hope it helps, Regards, ======================================================== Gonzalo Jimnez-Oss Complejo Cientfico Tecnolgico Departamento de Qumica. Universidad de La Rioja Grupo de Sntesis Qumica de la Rioja, U.A.-C.S.I.C. C/ Madre de Dios, 51. E-26006 Logroo (La Rioja). Spain Tfn. +34-941-299630 Fax +34-941-299621 gonzalo.jimenez .. unirioja.es http://www.unirioja.es/cu/gojimeo ======================================================== ------------------------ Sent to CCL by: "Nihan Aldis" [naldis ~~ gmail.com] Dear CCLers, When I use gen keyword in Oniom calculation on a Silicon cluster, I have some problems. This is part of my input: RunGauss %chk=Si353Gen2 %nproc=1 %mem=1000MB p opt oniom(b3lyp/Gen:am1/sparse) gfinput iop(6/7=3) gen 0 1 0 1 0 1 Si 0 1.724600 -4.250418 1.968610 H Si 0 3.751190 -3.034175 1.924736 L H 1 Si 0 5.662891 -4.357333 1.929145 L Si 0 6.231758 -5.525771 3.838685 L Si 0 8.593935 -5.661679 3.806473 L Si 0 9.324290 -4.582704 5.732750 L Si 0 11.401024 -3.435620 5.647742 L Si 0 11.390783 -1.944169 3.792553 L Si 0 9.600614 -0.392726 3.864778 L Si 0 9.613309 0.972654 1.922365 L Si 0 9.567945 -0.388159 0.000714 L Si 0 9.613275 0.961448 -1.928825 L Si 0 9.600508 -0.415218 -3.863267 L Si 0 11.390636 -1.966275 -3.782136 L ...................... ........................ H 0 0.000606 14.105707 3.098136 L H 0 1.190799 15.481702 -0.037854 L H 0 -1.202043 15.474212 -0.037516 L 40 50 107 140 152 160 0 6-31G* **** 1 41 51 76 93 94 108 131 0 3-21G* **** 132 141 153 161 169 175 185 0 3-21G* **** When it ran, I got the following error in the output: Warning! H atom 172 has 1 valence electrons but only 0 basis functions. This is less than a minimal basis set! Warning! H atom 176 has 1 valence electrons but only 0 basis functions. This is less than a minimal basis set! Warning! H atom 182 has 1 valence electrons but only 0 basis functions. This is less than a minimal basis set! Warning! H atom 186 has 1 valence electrons but only 0 basis functions. This is less than a minimal basis set! Warning! H atom 195 has 1 valence electrons but only 0 basis functions. This is less than a minimal basis set! IExCor= 402 DFT=T Ex=B+HF Corr=LYP ExCW=0 ScaHFX= 0.200000 ScaDFX= 0.800000 0.720000 1.000000 0.810000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 334 NActive= 41 NUniq= 41 SFac= 1.00D+00 NAtFMM= 60 Big=F Leave Link 301 at Fri Jul 27 15:31:01 2007, MaxMem= 131072000 cpu: 0.0 (Enter /home/g03/l302.exe) ........................ ........................... >>>>>>>>>> Convergence criterion not met. SCF Done: E(RB+HF-LYP) = -6064.80456753 A.U. after 129 cycles Convg = 0.8803D-04 -V/T = 2.0032 S**2 = 0.0000 KE= 6.045687912820D+03 PE=-2.555956789915D+04 EE= 7.901465986937D+03 Convergence failure -- run terminated. Error termination via Lnk1e in /home/g03/l502.exe at Sat Jul 28 13:38:31 2007. Job cpu time: 0 days 22 hours 6 minutes 44.1 seconds. File lengths (MBytes): RWF= 669 Int= 0 D2E= 0 Chk= 391 Scr= 1 What can I do to use both the ONIOM and the gen keyword? Is there anything to add my input? Thank you Nihan Aldishttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- No virus found in this incoming message. Checked by AVG Free Edition. Version: 7.5.476 / Virus Database: 269.10.25/926 - Release Date: 29/07/2007 23:14 From owner-chemistry@ccl.net Tue Jul 31 09:55:00 2007 From: "Andrew Turner andrew.turner|a|ed.ac.uk" To: CCL Subject: CCL:G: Optimized molecules - Draw Message-Id: <-34835-070731042721-24024-v3oAgysm9gcjYmprNgE/qA-,-server.ccl.net> X-Original-From: Andrew Turner Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 31 Jul 2007 08:56:11 +0100 MIME-Version: 1.0 Sent to CCL by: Andrew Turner [andrew.turner()ed.ac.uk] Try Platon. I used to use it to generate exactly those sort of pictures: http://www.chem.gla.ac.uk/~louis/software/platon/ Andy Mohamed Imran PK imranpkm*gmail.com wrote: > Sent to CCL by: "Mohamed Imran PK" [imranpkm .. gmail.com] > > To me this looks like the 3 D coordinates have been used by the > program ORTEP to generate this type of picture. > > Imran > > On 7/28/07, John Merle jkmerle~~yahoo.com wrote: >> Sent to CCL by: John Merle [jkmerle(_)yahoo.com] >> Mike, >> >> This figure looks to have been generated by either >> Molecule or Ball and Stick. Both are Mac programs and >> are still available but are no longer being developed. >> >> John Merle >> --- "Mike hang mikehang2007*yahoo.com" >> wrote: >> >>> Dear CCL users >>> >>> can you people tell me which software has been used >>> to draw the following molecule >>> >>> click on link below >>> >>> >> http://img2.freeimagehosting.net/image.php?89ebec4e78.jpg >>> also can someone recommend me a software that can >>> make colorless, editable and publishable drawing of >>> optimized geometry a molecule generated by >>> Gaussview/Gaussian 03 >>> >>> >>> --------------------------------- >>> Ready for the edge of your seat? Check out tonight's >>> top picks on Yahoo! TV. >> >> >> >> ____________________________________________________________________________________ >> Boardwalk for $500? In 2007? Ha! Play Monopoly Here and Now (it's updated for today's economy) at Yahoo! Games. >> http://get.games.yahoo.com/proddesc?gamekey=monopolyherenow> > > > -- ================================== Dr Andrew R. Turner Research Computing Officer e: andrew.turner _ ed.ac.uk t: +44 (0)131 650 7748 w: http://www.eastchem.ac.uk/rcf icq: 370-899-715 p: School of Chemistry University of Edinburgh EH9 3JJ ================================== From owner-chemistry@ccl.net Tue Jul 31 11:27:00 2007 From: "Loan Huynh huynhkl2000:_:yahoo.ca" To: CCL Subject: CCL: Program to fit the Fourier Series - software for equipotential lines Message-Id: <-34836-070731111832-30994-FJWn9HttILgkWwuv9rFtXg-.-server.ccl.net> X-Original-From: Loan Huynh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1124110717-1185895084=:85619" Date: Tue, 31 Jul 2007 11:18:04 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000]|[yahoo.ca] --0-1124110717-1185895084=:85619 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Hoa and Igor, Thanks for the advice. I installed free Matlab software and free Gnuplot software. I found that gnuplot is a bit easier to use. Although, I don't know which one is better. Micheal, you may one to check out Gnuplot. It's free and for window. You can find it at: http://www.gnuplot.info/ good lucks. Loan "Hoa Nguyen hoagiaonguyen%yahoo.com" wrote: Hi Loan, Give Matlab a try. It has a Curve Fitting toolbox. The command is "cftool". Good luck, Hoa Nguyen Department of Chemistry University of Utah "Loan Huynh huynhkl2000(a)yahoo.ca" wrote: Hi all, Does anyone know any program that can be used to fit the Fourier series into know values? Any recommendation is greatly aprreciated! Fourier Transform: Vrb(fijkl) = V0 + 1/2(V1(1 + cos(y)) + V2(1 − cos(2y)) + V3(1 + cos(3y))) Many thanks, Loan --------------------------------- Choose the right car based on your needs. Check out Yahoo! Autos new Car Finder tool. --0-1124110717-1185895084=:85619 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Hoa and Igor,
Thanks for the advice.  I installed free Matlab software and free Gnuplot software.  I found that gnuplot is a bit easier to use.  Although, I don't know which one is better. 
Micheal, you may one to check out Gnuplot.  It's free and for window.  You can find it at: http://www.gnuplot.info/
good lucks.
Loan

"Hoa Nguyen hoagiaonguyen%yahoo.com" <owner-chemistry]^[ccl.net> wrote:
Hi Loan,
 
Give Matlab a try. It has a Curve Fitting toolbox. The command is "cftool".
 
Good luck,
 
Hoa Nguyen
Department of Chemistry
University of Utah

"Loan Huynh huynhkl2000(a)yahoo.ca" <owner-chemistry]*[ccl.net> wrote:
Hi all,
 
Does anyone know any program that can be used to fit the Fourier series into know values?  Any recommendation is greatly aprreciated!
 
Fourier Transform:
Vrb(fijkl) = V0 + 1/2(V1(1 + cos(y)) + V2(1 − cos(2y)) + V3(1 + cos(3y)))

Many thanks,
Loan

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--0-1124110717-1185895084=:85619-- From owner-chemistry@ccl.net Tue Jul 31 23:49:00 2007 From: "sabri alkis alkis/a\ufl.edu" To: CCL Subject: CCL: dlpoly error Message-Id: <-34837-070731162658-26723-vwVghj8Q2InYw3btrasMpg_-_server.ccl.net> X-Original-From: "sabri alkis" Date: Tue, 31 Jul 2007 16:26:54 -0400 Sent to CCL by: "sabri alkis" [alkis ~~ ufl.edu] Hi everyone, I have alkanthiol monolayer (12 carbon molecule, linear chain)on gold surface. I put gold atoms on top of the monolayer. When I do the simulation some atoms cluster and some atoms go down inside the layer. The problem is, the simulation runs a little bit then I get the error message "1-4 separation exceeds cutoff". I remember getting this error before, at that time, it was because of the boundary conditions and I fixed it. I do not think it is due to dihedral angles this time.. Is it like some gold atoms are coming too close to carbons,hydrogens? Does anyone have an idea? Can you guys please help me out? regards,