From owner-chemistry@ccl.net Sat May 26 00:30:01 2012 From: "Esteban Gabriel Vega Hissi egvega-x-gmail.com" To: CCL Subject: CCL: Optimization Conformation? Message-Id: <-46990-120525231817-4962-zmPBCltvtzIdfjJ3XBYuGg- -server.ccl.net> X-Original-From: Esteban Gabriel Vega Hissi Content-Type: multipart/alternative; boundary=f46d0446318003edba04c0e7ef38 Date: Sat, 26 May 2012 00:17:46 -0300 MIME-Version: 1.0 Sent to CCL by: Esteban Gabriel Vega Hissi [egvega|,|gmail.com] --f46d0446318003edba04c0e7ef38 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, With a frequency calculation and checking for the absence of imaginary frequencies. On Fri, May 25, 2012 at 12:49 PM, Asif Mahmood eminabadi(!)yahoo.com < owner-chemistry,+,ccl.net> wrote: > > Sent to CCL by: "Asif Mahmood" [eminabadi,+,yahoo.com] > How I can confirm the successful optimization of a structure after a > normal termination of optimization job. > > Advance thanks > > Asif Mahmood > > Pakistan > > eminabadi*yahoo.com > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Esteban Gabriel Vega Hissi =C1rea de Qu=EDmica F=EDsica Departamento de Qu=EDmica Universidad Nacional de San Luis Argentina --f46d0446318003edba04c0e7ef38 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi,

With a frequency calculation and checking for the ab= sence of imaginary frequencies.


On Fri, May 25, 2012 at 12:49 PM, Asif Mahmood eminabadi(!)yahoo.com <owner-chemistry,+,ccl.net= > wrote:

Sent to CCL by: "Asif =A0 Mahmood" [eminabadi,+,yahoo.com]
How I can confirm the successful optimization of a structure after a normal= termination of optimization job.

Advance thanks

Asif Mahmood

Pakistan

eminabadi*yahoo.com



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Esteban Gabr= iel Vega Hissi
=C1rea de Qu=EDmica F=EDsica
Departamento de Qu=EDmica=
Universidad Nacional de San Luis
Argentina

--f46d0446318003edba04c0e7ef38-- From owner-chemistry@ccl.net Sat May 26 13:03:01 2012 From: "Andrew Yeung andrew.yeung,,chem.tamu.edu" To: CCL Subject: CCL: Optimization Conformation? Message-Id: <-46991-120526000321-782-QbatgS/iXInEYditWubNMw * server.ccl.net> X-Original-From: Andrew Yeung Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 25 May 2012 23:03:12 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Yeung [andrew.yeung{=}chem.tamu.edu] Check that first of all, the structure makes chemical sense. Check that it has achieved the four convergence criteria (max & RMS force and displacement), and that it says something about convergence reached. Do a frequency calculation, and verify that there are no imaginary modes (NImag=0 in the archive). Andrew Yeung Donald J. Darensbourg Research Group Department of Chemistry, Texas A&M University 3255 TAMU College Station, TX 77843-3255 Tel: 979 845 4837 On 2012-05-25 10:49 AM, Asif Mahmood eminabadi(!)yahoo.com wrote: > Sent to CCL by: "Asif Mahmood" [eminabadi,+,yahoo.com] > How I can confirm the successful optimization of a structure after a normal termination of optimization job. > > Advance thanks > > Asif Mahmood > > Pakistan > > eminabadi*yahoo.com> > From owner-chemistry@ccl.net Sat May 26 13:38:01 2012 From: "Gonzalo Jimenez Oses gonzalo.jimenez(~)unirioja.es" To: CCL Subject: CCL: Optimization Conformation? Message-Id: <-46992-120526012623-1175-YpTkGrkpK+OLp4Fhu0z+dw+*+server.ccl.net> X-Original-From: "Gonzalo Jimenez Oses" Date: Sat, 26 May 2012 01:26:22 -0400 Sent to CCL by: "Gonzalo Jimenez Oses" [gonzalo.jimenez]=[unirioja.es] Hi, When I read this kind of facepalm questions I still cannot believe why is so apparently difficult to read free online manuals, tutorials, how-to's, faq's on such extremely basic and fundamental things. Sorry, but I wouldn't trust any result coming from (or worse, published by) anybody who does know what is he/she doing before submitting the calculation of running the experiment. What about throwing a piece of sodium into water just to see what happens? And then ask someone at one experimental chemistry forum what to do if things go bad... I truly wouldn't want to hurt anyone's feelings and I am aware about the limitations to access some resources in some places, but to me this is not an excuse to have a 30-seconds look at the free online manual of the software you are using. As I said so many times before, to me this is a generational-educational-social problem. Apparently, it is easier to ask for everything than to do a little bit of self-teaching. I encourage everyone to READ books, papers and manuals before posting. It is really pleasant to solve problems on one's own, and in the process of finding the solution you really learn a lot! My two cents, Gonzalo > "Asif Mahmood eminabadi(!)yahoo.com" wrote: > > Sent to CCL by: "Asif Mahmood" [eminabadi,+,yahoo.com] > How I can confirm the successful optimization of a structure after a normal termination of optimization job. > > Advance thanks > > Asif Mahmood > > Pakistan > > eminabadi..yahoo.com > > From owner-chemistry@ccl.net Sat May 26 14:13:00 2012 From: "sobereva sobjubao~!~yahoo.com.cn" To: CCL Subject: CCL: 2D Electrostatic Potential map Message-Id: <-46993-120526020431-1338-kBcj5DeJaf8KcqDlvBZjuQ###server.ccl.net> X-Original-From: sobereva Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 26 May 2012 14:04:21 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: sobereva [sobjubao]-[yahoo.com.cn] Hi, Multiwfn can do this, which can be freely downloaded at http://Multiwfn.codeplex.com. First of all, you need to write a plain text file containing atomic charges and then save the file with .chg extension. An example for H2O2 is given below, the first three columns correspond to xyz coordinates(in Angstrom), the last column is atomic charge. O 0.000000 0.698232 -0.054644 -0.417690 H -0.787194 0.896852 0.437152 0.417691 O 0.000000 -0.698232 -0.054644 -0.417690 H 0.787194 -0.896852 0.437152 0.417691 Then boot up Multiwfn and input below commands in turn: h2o2.chg // The path of .chg file 4 // Plotting 2D map 8 // ESP from atomic charges 2 // Contour map, you can also choose other types such as relief map, color-filled map Press ENTER button to use default grid setting 4 // Define the plane by three atoms, you can also define the plane in other ways by choosing corresponding options 1,3,4 // Use atom 1,3,4 to define the plane The 2D ESP map will pop up immediately, you can click right mouse button on the window to close it, and then refine the map by corresponding options. By the way, the plane data generated by Multiwfn can be directly exported to .txt file, therefore you can easily redraw the map by some third-part visualization softwares such as Sigmaplot, Surfer and Origin. Best wishes, Tian Lu School of Chemical and Biological Engineering University of Science and Technology Beijing No.30, XueYuan road, HaiDian district, Beijing, P. R. China mailto: sobereva:_:sina.com --- On Sat, 5/26/12, Eliac Brown Eliacbrown*yahoo.com wrote: > From: Eliac Brown Eliacbrown*yahoo.com > Subject: CCL: 2D Electrostatic Potential map > To: "Lu, Tian " > Date: Saturday, May 26, 2012, 4:29 AM > > Sent to CCL by: "Eliac  Brown" > [Eliacbrown#%#yahoo.com] > Dear All > In a part of my project, we need to generate the > electrostatic potential map > for some molecules using pre-calculated charges. The > conventional way to draw > the electrostatic maps is to generate the density and > potential cubes and load > them in a visualization program. While, here we want to > generate the > electrostatic map using a new set of charges. Do you know > any software that can  > be used to perform this job? > I was also wondering if you could tell me which program can > be used to draw 2D > electrostatic map (not 3D grid). > Any kind of help would be appreciated > Cheers > E. Brown > > > > -= 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> > E-mail to subscribers: CHEMISTRY:_:ccl.net > or use: >      > > E-mail to administrators: CHEMISTRY-REQUEST:_:ccl.net > or use >      >      >      > > > From owner-chemistry@ccl.net Sat May 26 14:48:00 2012 From: "mozhdeh Mohamadpour mozhdehmohammadpour_._gmail.com" To: CCL Subject: CCL: A problem using Sapt2008 Message-Id: <-46994-120526034524-1865-YCwBaDNTD828zT9H2EJ4Kw]~[server.ccl.net> X-Original-From: "mozhdeh Mohamadpour" Date: Sat, 26 May 2012 03:45:23 -0400 Sent to CCL by: "mozhdeh Mohamadpour" [mozhdehmohammadpour ~~ gmail.com] Dear Subscribers I have used a Saptdft calculation for a system of a krypton dimer (KrKr) with specifying basis sets by ATOMBASIS( aug-ccPvdz) which I could not get results when it came to tran subroutines, It seems that there are some files which they cannot be found and because of this the program has been aborted. I would be grateful if you could look in the following paragraphs including saptdft error message of my output, and reply me how we could overcome this problem. ################################################################### #### Run Transformation program. #### ################################################################### Kr-Kr &TRN ISITALCH=F, ISITG88=F, ISITG90=F, ISITHNDO=F, ISITMICR=F, ISITANEW=F, ISITDALT=T, OUT=F, TOLER=15, SPHG=T, DIMER=F, MEMTRAN=500000000, BLKMB=F, basis='sssssppppddssspppddsssssppppdd+', tags='mmmmmmmmmaammmmmmmmmmmmmmmmmbb+' &END &CCINP CCPRINT=F, VCRIT=1.0D-14, TOLITER=1.0D-12 &END &INPUTCOR SAPTKS=T, PRINT=F, MEMSAPT=40000000 &END &SAPTDFT CKSDISP=T, CKSIND=T &END rm: cannot remove `docc': No such file or directory -------------------------------------------------- GENERAL N5 TRANSFORMATION PROGRAM Sequential Version. Copyright (C) 1990. S. Rybak Copyright (C) 1996-2008 R. Bukowski, W. Cencek, P. Jankowski, M. Jeziorska, B. Jeziorski, S. A. Kucharski, V. F. Lotrich, A. J. Misquitta, R. Moszynski, K. Patkowski, R. Podeszwa, S. Rybak, K. Szalewicz, H. L. Williams, R. J. Wheatley, P. E. S. Wormer, and P. S. Zuchowski. All rights reserved. Part of SAPT suite. Version 2008.2 -------------------------------------------------- ------------------------------------ Requested memory is 500000000 words ------------------------------------ f90 allocated 500000000 words Memory allocation looks like it succeeded forrtl: No such file or directory forrtl: severe (29): file not found, unit 2, file /home/workshop/KrKr-ds/vectb.data Image PC Routine Line Source tran 00000000004DB73A Unknown Unknown Unknown tran 00000000004DA2B5 Unknown Unknown Unknown tran 00000000004886D6 Unknown Unknown Unknown tran 000000000042C305 Unknown Unknown Unknown tran 000000000042BAC1 Unknown Unknown Unknown tran 000000000043D381 Unknown Unknown Unknown tran 000000000040CA19 Unknown Unknown Unknown tran 000000000041540F Unknown Unknown Unknown tran 0000000000414CCB Unknown Unknown Unknown tran 000000000040E263 Unknown Unknown Unknown tran 000000000040390C Unknown Unknown Unknown libc.so.6 00007F080DABBAFD Unknown Unknown Unknown tran 0000000000403809 Unknown Unknown Unknown Command exited with non-zero status 29 0.00user 0.00system 0:00.00elapsed 0%CPU (0avgtext+0avgdata 14720maxresident)k 0inputs+0outputs (0major+986minor)pagefaults 0swaps total 15400 drwxrwxr-x 2 workshop workshop 4096 2009-05-24 11:42 . drwxr-xr-x 38 workshop workshop 4096 2009-05-24 11:41 .. -rw-r--r-- 1 workshop workshop 92756 2009-05-24 11:42 AOONEINT -rw-r--r-- 1 workshop workshop 7519 2009-05-24 11:42 DALTON.BAS -rwxr-xr-x 1 workshop workshop 411 2009-05-24 11:42 file5.dat -rw-r--r-- 1 workshop workshop 3002704 2009-05-24 11:42 h1A.data -rw-r--r-- 1 workshop workshop 0 2009-05-24 11:42 h2A.data -rw-r--r-- 1 workshop workshop 0 2009-05-24 11:42 h2B.data -rw-r--r-- 1 workshop workshop 106 2009-05-24 11:42 infoa.data -rw-r--r-- 1 workshop workshop 69 2009-05-24 11:42 infob.data -rw-r--r-- 1 workshop workshop 13 2009-05-24 11:42 info.data -rw-r--r-- 1 workshop workshop 12051388 2009-05-24 11:42 inta.data -rw-r--r-- 1 workshop workshop 35 2009-05-24 11:42 interface.input -rwxr-xr-x 1 workshop workshop 227 2009-05-24 09:08 KrKr-dsA.dal -rwxr-xr-x 1 workshop workshop 7172 2009-05-24 10:54 KrKr-dsA.mol -rwxr-xr-x 1 workshop workshop 234 2009-05-24 09:09 KrKr-dsB.dal -rwxr-xr-x 1 workshop workshop 7177 2009-05-24 10:54 KrKr-dsB.mol -rwxr-xr-x 1 workshop workshop 267 2009-05-24 09:09 KrKr-dsMA.dal -rwxr-xr-x 1 workshop workshop 7047 2009-05-24 10:53 KrKr-dsMA.mol -rwxr-xr-x 1 workshop workshop 267 2009-05-24 09:09 KrKr-dsMB.dal -rwxr-xr-x 1 workshop workshop 7047 2009-05-24 10:53 KrKr-dsMB.mol -rw-r--r-- 1 workshop workshop 84928 2009-05-24 11:42 KrKr-ds.out.ifort -rwxr-xr-x 1 workshop workshop 411 2009-05-24 11:40 KrKr-dsP.data -rwxr-xr-x 1 workshop workshop 418 2009-05-24 11:17 KrKr-dsP.data~ -rw-r--r-- 1 workshop workshop 21 2009-05-24 11:42 ksi.data -rw-r--r-- 1 workshop workshop 93712 2009-05-24 11:42 onela.data -rw-r--r-- 1 workshop workshop 93712 2009-05-24 11:42 onelb.data -rw-r--r-- 1 workshop workshop 26 2009-05-24 11:42 scfener.data.dalton -rw-r--r-- 1 workshop workshop 151004 2009-05-24 11:42 SIRIFC -rw-r--r-- 1 workshop workshop 46448 2009-05-24 11:42 SIRIUS.RST -rw-r--r-- 1 workshop workshop 35392 2009-05-24 11:42 vecta.data Sincerely yours