From owner-chemistry@ccl.net Sat Sep 12 04:37:01 2009 From: "Andreas Klamt klamt:+:cosmologic.de" To: CCL Subject: CCL: the dynamic (or optical) dielectric constant of the solvent(EpsInf). Message-Id: <-40235-090912040852-19010-FD5eaQUjUmALNAryVa0QjQ|*|server.ccl.net> X-Original-From: Andreas Klamt Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sat, 12 Sep 2009 10:08:38 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Klamt [klamt~!~cosmologic.de] Dear Ajitha, half a year ago I did a search on that because I wanted to have these=20 properties available for some further improvements of the COSMO-RS=20 method in our COSMotherm program. The result was somewhat disappointing. For the optical epsilon the situation is not too bad. Basically it can=20 be calculated from the electronic polarizabilities, but you also need a=20 density prediction, ... Essentially some incremental schemes based on=20 atom information and count of double bonds + a density estimate yield=20 acceptable quality. You do not really need DFT for that. I ended up with = some method similar to whar Leo and Hansch have as their CMR method in=20 the CLOGP program. Indeed, I doubt that one will be more accurate using D= FT. The situation is much more complicated for the static dielectric=20 constant eps(0). You need to take into account dipole moments, but not=20 just of the compound in the ground state, but also of a large number of=20 conformations. Otherwise you would get zero contributions from=20 reorientational polarizability for compounds which are flexible, but=20 have a symmetric minimum energy conformation (and hence zero dipole=20 moment), e.g. 1,4-butan-di-ol. You would get all of them just have=20 eps(0) =3D eps(inf). And that is rubbish. Applying an automated analysis of flexible bonds, a DFT/COSMO analysis=20 of the partial dipole moments on both sides of the flexible bonds, and=20 an approximate MC simulation for getting from this a kind of average for = the total dipole moment, and combined with the estimate of eps(infinity) = for the electronic polarizability, I finally yielded a reasobable=20 description of the dielectric constant of a wide range of liquids. This is not yet available as standard feature in our COSMotherm program, = but we could discuss how to make it available. Andreas John ajitha Manjaly aji.john07,gmail.com schrieb: > Sent to CCL by: "John ajitha Manjaly" [aji.john07(0)gmail.com] > Dear Friends, > > It will be very useful for me to know about the calculation of the dyna= mic (or optical) dielectric constant(EpsInf)of a solvent(say methanol). I= s there any DFT method to calculate the same?=20 > > Thanking you, > Ajitha > > > > -=3D This is automatically added to each message by the mailing script = =3D- > To recover the email address of the author of the message, please chang= e> > Subscribe/Unsubscribe:=20> > Job: http://www.ccl.net/jobs=20=> > > > =20 --=20 PD. Dr. Andreas Klamt CEO / Gesch=E4ftsf=FChrer COSMOlogic GmbH & Co. KG Burscheider Strasse 515 D-51381 Leverkusen, Germany phone +49-2171-731681 fax +49-2171-731689 e-mail klamt(a)cosmologic.de web www.cosmologic.de HRA 20653 Landgericht Koeln, GF: Dr. Andreas Klamt Komplementaer: COSMOlogic Verwaltungs GmbH HRB 49501 Landgericht Koeln, GF: Dr. Andreas Klamt From owner-chemistry@ccl.net Sat Sep 12 11:05:00 2009 From: "Serdar Badošlu sbadoglu**gazi.edu.tr" To: CCL Subject: CCL:G: Current density map Message-Id: <-40236-090912110306-9270-yRXYU5JebpNCIX28qZrMBw(0)server.ccl.net> X-Original-From: "Serdar Badošlu" Date: Sat, 12 Sep 2009 14:34:51 -0000 Sent to CCL by: "Serdar Badošlu" [sbadoglu^gazi.edu.tr] Hi Tian, I hope this link may help you: http://faculty.ycp.edu/~jforesma/educ/visual/index.html "Green Power powergreen]^[gmail.com" dedi: > Hi, All > > Anybody know how to visualize the current density map generalized by > Gaussian cube file? In a previous message on the CCL, it is said CCP1GUI can > do that. But there is little documentation for this package and I could not > figure how to to do that. Could you give me any instructions if you have any > experience about that. Thank you in advance. > > Tian > -- Serdar BADOGLU http://docs.google.com/View?id=dckx8v2c_286bpvdsdt From owner-chemistry@ccl.net Sat Sep 12 14:38:01 2009 From: "Nilesh Tawari tawari.nilesh[a]gmail.com" To: CCL Subject: CCL: Visualizer for MOPAC Message-Id: <-40237-090912143657-15016-BZ3ZruyQLjACxJ1vDIoyRw() server.ccl.net> X-Original-From: "Nilesh Tawari" Date: Sat, 12 Sep 2009 14:36:53 -0400 Sent to CCL by: "Nilesh Tawari" [tawari.nilesh|-|gmail.com] Hello everybody, I want to know any good program for the visualization of various files generated using MOPAC2009. Files include .esp, .esr, .den, .mgf, .arc and .gpt. Avagadro doesn't work with these files. Kindly help -nilesh From owner-chemistry@ccl.net Sat Sep 12 16:43:00 2009 From: "Stephen Bowlus chezbowlus_._comcast.net" To: CCL Subject: CCL: Visualizer for MOPAC Message-Id: <-40238-090912162037-14180-lojTyWBmB8MISMWxaLh6Ug]^[server.ccl.net> X-Original-From: Stephen Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Sat, 12 Sep 2009 12:47:38 -0700 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Stephen Bowlus [chezbowlus|a|comcast.net] Please post a summary of your replies. I, too, am looking for a simple visualizer for general chemistry students that will handle MOPAC and GAMESS and/or Firefly output. Steve Bowlus Columbia College On Sep 12, 2009, at 11:36 AM, Nilesh Tawari tawari.nilesh[a]gmail.com wrote: > > Sent to CCL by: "Nilesh Tawari" [tawari.nilesh|-|gmail.com] > Hello everybody, > I want to know any good program for the visualization of various > files generated using MOPAC2009. Files > include .esp, .esr, .den, .mgf, .arc and .gpt. > Avagadro doesn't work with these files. > > Kindly help > -nilesh > > > > -= 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/> > From owner-chemistry@ccl.net Sat Sep 12 18:23:00 2009 From: "Marcus D. Hanwell marcus\a/cryos.org" To: CCL Subject: CCL: Visualizer for MOPAC Message-Id: <-40239-090912182101-14410-zIgGg+mGKfl+DFtBNHoIyQ[]server.ccl.net> X-Original-From: "Marcus D. Hanwell" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 12 Sep 2009 17:50:18 -0400 MIME-Version: 1.0 Sent to CCL by: "Marcus D. Hanwell" [marcus!=!cryos.org] Nilesh Tawari tawari.nilesh[a]gmail.com wrote: > Sent to CCL by: "Nilesh Tawari" [tawari.nilesh|-|gmail.com] > Hello everybody, > I want to know any good program for the visualization of various files generated using MOPAC2009. Files include .esp, .esr, .den, .mgf, .arc and .gpt. > Avagadro doesn't work with these files. > > If you use the AUX keyword then Avogadro should work fine with MOPAC2009 output. I need to add a reader to OpenBabel in order to streamline the process of loading MOPAC output. Currently you have to load the output file, and if you want to visualize the surface Avogadro scans the directory for a file with the same name but an aux file extension. I was looking at possibly adding support for mgf, but my understanding is that the aux file is the preferred file for visualization programs to use. Adding the AUX keyword to the input file, or using Avogadro to generate the input file will ensure MOPAC produces the file Avogadro needs. Marcus From owner-chemistry@ccl.net Sat Sep 12 18:59:01 2009 From: "=?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= jgcj_._fct.unl.pt" To: CCL Subject: CCL: Visualizer for MOPAC Message-Id: <-40240-090912180930-13591-xQk0F51WPeApkYf8pBl1ZA- -server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= Content-Type: multipart/alternative; boundary=0015173ff2e0e9f3d20473680932 Date: Sat, 12 Sep 2009 22:23:06 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Gon=E7alo_C=2E_Justino?= [jgcj_-_fct.unl.pt] --0015173ff2e0e9f3d20473680932 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Jmol (*jmol*.sourceforge.net) can read at least the gpt files.g. --=20 Gon=E7alo Justino, PhD, MSc ---------------------------------------------------- [Computational & Radical BioChemistry] Requimte/CQFB - Department of Chemistry Faculty of Sciences and Technology New University of Lisbon 2829-516 Caparica Portugal Phone: (+351) 212 948 300 ext. 10971 Fax: (+351) 212 948 550 ---------------------------------------------------- All saints have a past, all sinners have a future. 2009/9/12 Nilesh Tawari tawari.nilesh[a]gmail.com > > Sent to CCL by: "Nilesh Tawari" [tawari.nilesh|-|gmail.com] > Hello everybody, > I want to know any good program for the visualization of various files > generated using MOPAC2009. Files include .esp, .esr, .den, .mgf, .arc and > .gpt. > Avagadro doesn't work with these files. > > Kindly help > -nilesh > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --0015173ff2e0e9f3d20473680932 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Jmol (jmol.sourceforge.net) ca= n read at least the gpt files.
g.
--
Gon=E7alo Jus= tino, PhD, MSc
----------------------------------------------------
[Computational &= ; Radical BioChemistry]
Requimte/CQFB - Department of Chemistry
Facul= ty of Sciences and Technology
New University of Lisbon
2829-516 Capar= ica
Portugal
Phone: (+351) 212 948 300 ext. 10971
Fax: (+351) 212 948 550=
----------------------------------------------------
All saints have= a past, all sinners have a future.


2009/9/12 Nilesh Tawari tawari.nilesh[a]= gmail.com <owner-chemistry|-|ccl.net>
=

Sent to CCL by: "Nilesh =A0 Tawari" [tawari.nilesh|-|gmail.com]
Hello everybody,
I want to know any good program for the visualization of various files gene= rated using MOPAC2009. Files include .esp, .esr, .den, .mgf, .arc and .gpt.=
Avagadro doesn't work with these files.

Kindly help
-nilesh



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY|-|ccl.n= et or use:
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--0015173ff2e0e9f3d20473680932-- From owner-chemistry@ccl.net Sat Sep 12 23:08:01 2009 From: "DIEGOI GOMEZ darkego21{:}yahoo.com" To: CCL Subject: CCL: Visualizer for MOPAC Message-Id: <-40241-090912223740-2306-JulwBGzs4E1ASkLE0T+sNw..server.ccl.net> X-Original-From: DIEGOI GOMEZ Content-Type: multipart/alternative; boundary="0-911900180-1252805844=:24232" Date: Sat, 12 Sep 2009 18:37:24 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: DIEGOI GOMEZ [darkego21\a/yahoo.com] --0-911900180-1252805844=:24232 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hello..=0A=0AWith MOLDEN you can see the structural information from the .a= rc=A0 or .out files when the imput=A0(.mop)=A0is in z-matrix format.=A0 If = the imput is in=A0XYZ=A0coodinates you can see the .out file only. Addition= aly with MOLDEN is posible to create the=A0imput file for MOPAC2009.=A0 For= the .esp or .mgf you can use Jmol.=0A=0A=0A=0A=0A_________________________= _______=0AFrom: Nilesh Tawari tawari.nilesh[a]gmail.com =0ATo: "Gomez, Diego Armando " =0ASent: = Saturday, September 12, 2009 8:36:53 PM=0ASubject: CCL: Visualizer for MOPA= C=0A=0A=0ASent to CCL by: "Nilesh=A0 Tawari" [tawari.nilesh|-|gmail.com]=0A= Hello everybody, =0AI want to know any good program for the visualization o= f various files generated using MOPAC2009. Files include .esp, .esr, .den, = .mgf, .arc and .gpt.=0AAvagadro doesn't work with these files. =0A=0AKindly= help=0A-nilesh=0A=0A=0A=0A-=3D This is automatically added to each message= by the mailing script =3D-=0ATo recover the email address of the author of= the message, please change=0Athe strange characters on the top line to the= (0) sign. You can also=0Alook up the X-Original-From: line in the mail heade= r.=0A=0A=0A=A0 =A0 =A0 http= ://www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0AE-mail to administrators: = CHEMISTRY-REQUEST(0)ccl.net or use=0A=A0 =A0 =A0 http://www.ccl.net/cgi-bin/c= cl/send_ccl_message=0A=0A=0A=A0 =A0 =A0 http://www.c= cl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait time at: h= ttp://www.ccl.net=0A=0A=0AConferences: http://= server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Messages: h= ttp://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail bounces= from CCL with 5.7.1 error, check:=0A=A0 =A0 =A0 http://www.ccl.net/spammer= s.txt=0A=0A=0A=0A= =0A --0-911900180-1252805844=:24232 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hello..
=0A
 
=0A
With MOLDEN you can see = the structural information from the .arc  or .out files when the imput=  (.mop) is in z-matrix format.  If the imput is in XYZ&= nbsp;coodinates you can see the .out file only. Additionaly with MOLDEN is = posible to create the imput file for MOPAC2009.  For the .esp or = .mgf you can use Jmol.
=0A

=0A
=0A=0AFrom: Nilesh T= awari tawari.nilesh[a]gmail.com <owner-chemistry(0)ccl.net>
To: "Gomez, Diego Armando "= <darkego21(0)yahoo.com>
Sent:<= /SPAN> Saturday, September 12, 2009 8:36:53 PM
Subject: CCL: Visualizer for MOPAC

Sent to CCL by: "Nilesh  Tawari" [tawari.nilesh|-|gmail.com]
H= ello everybody,
I want to know any good program for the visualization o= f various files generated using MOPAC2009. Files include .esp, .esr, .den, = .mgf, .arc and .gpt.
Avagadro doesn't work with these files.

Kin= dly help
-nilesh



-=3D This is automatically added to each= message by the mailing script =3D-
To recover the email address of the = author of the message, please change
the strange characters on the top l= ine to the (0) sign. You can also<= BR>E-mail to subscribers: CHEMISTRY(0)ccl.net or use:
    &nb= sp;

E-mail to admini= strators: CHEMISTRY-REQUEST(0)ccl.net or use
  &nb= sp;   http://www.ccl.net/cgi-bin/ccl/send_ccl_message

Subs= cribe/Unsubscribe:
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Conferences: http://server.ccl.net= /chemistry/announcements/conferences/

Search Messages: http://www.cc= l.net/chemistry/searchccl/index.shtml

If your mail bounces from CCL = with 5.7.1 error, check:
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<= BR>

=0A=0A=0A=0A --0-911900180-1252805844=:24232--