From owner-chemistry@ccl.net Thu Jun 24 02:43:00 2010 From: "Jon Fuller fbsjf=-=leeds.ac.uk" To: CCL Subject: CCL: GROMACS PROGRAM Message-Id: <-42159-100624024054-14588-0AQh6FE/YKWOvV8XugobHA() server.ccl.net> X-Original-From: Jon Fuller Content-Type: multipart/alternative; boundary=0015174befdc28c9c10489c0efff Date: Thu, 24 Jun 2010 07:40:45 +0100 MIME-Version: 1.0 Sent to CCL by: Jon Fuller [fbsjf[-]leeds.ac.uk] --0015174befdc28c9c10489c0efff Content-Type: text/plain; charset=ISO-8859-1 Dear Claudia, The best place to ask this question is probably the Gromacs users mailing list . Although you should search the list first based on simulating a ligand/small-molecule/compound in water. I am pretty certain that a variant on this question will have been asked before. Best, Jon On 23 June 2010 15:47, Claudia ------------- Escobar iqclaudia_428^_^ hotmail.com wrote: > > Sent to CCL by: "Claudia ------------- Escobar" [iqclaudia_428/./ > hotmail.com] > Dear all: > > I'm trying to make a run on GROMACS (molecular dynamics) but the system I > have is an aldehyde with alcohol. This program comes with tutorials only > protein and water as a solvent. Someone could help me. Thank you very much > > > > Claudia Escobar > > UTN-FRRE> > > --0015174befdc28c9c10489c0efff Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Claudia,

The best place to ask this question is pro= bably the=A0Gromacs users mailing list. Although you should search the= list first based on simulating a ligand/small-molecule/compound in water. = I am pretty certain that a variant on this question will have been asked be= fore.

Best,

Jon

On 23 June 2010 15:47, Claudia ------------- Escobar iqclaudi= a_428^_^hotmail.com &l= t;owner-chemistry]-[ccl.net>= ; wrote:

Sent to CCL by: "Claudia =A0------------- Escobar" [iqclaudia_428= /./hotmail.com]
Dear all:

I'm trying to make a run on GROMACS (molecular dynamics) but the system= I have is an aldehyde with alcohol. This program comes with tutorials only= protein and water as a solvent. Someone could help me. Thank you very much=



Claudia Escobar

UTN-FRRE



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--0015174befdc28c9c10489c0efff-- From owner-chemistry@ccl.net Thu Jun 24 08:25:01 2010 From: "John McKelvey jmmckel!^!gmail.com" To: CCL Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42160-100624081726-23538-zUfUj5h9O5ZahE99Nz7NbA .. server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 24 Jun 2010 08:17:18 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel,gmail.com] Hello, I have about 50 MOPAC input structures I need to get into 2D drawings for publication, obviously multiple drawings on a page. Any suggestions how to do this? Thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel!A!gmail.com From owner-chemistry@ccl.net Thu Jun 24 09:00:00 2010 From: "ABHISHEK SHAHI shahi.abhishek1984/a\gmail.com" To: CCL Subject: CCL:G: list of errors ??? Message-Id: <-42161-100623143611-26313-g8iCIXxTg7Rsgm+9z/6hTg!A!server.ccl.net> X-Original-From: ABHISHEK SHAHI Content-Type: multipart/alternative; boundary=000e0cd29c467aa7410489b6b73b Date: Wed, 23 Jun 2010 23:59:22 +0530 MIME-Version: 1.0 Sent to CCL by: ABHISHEK SHAHI [shahi.abhishek1984\a/gmail.com] --000e0cd29c467aa7410489b6b73b Content-Type: text/plain; charset=ISO-8859-1 Dear All Can we have a list of all error and their corresponding solutions in gaussian at one place . If some information regards to this then please send that link. I am new subscriber . So please send me the yahoo group ID by witch i can solve my problem with the help of our online member. what I have to do for this? Thanks a lot -- With regards; ABHISHEK SHAHI Ph. D. student :Mail To : shahi.abhishek1984^_^gmail.com --000e0cd29c467aa7410489b6b73b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear All
=A0=A0=A0=A0 Can we have a list of all error and their correspo= nding solutions in gaussian at one place . If some information regards to t= his then please send that link.
=A0 =A0 =A0=A0 I am new subscriber . So = please send me the yahoo group ID by witch i can solve my problem with the= =A0 help of our online member. what I have to do for this?
=A0=A0=A0=A0=A0 Thanks a lot
=A0=A0
--
With regar= ds;
=A0ABHISHEK SHAHI
=A0Ph. D. student
:Mail To : shahi.abhishek1984^_^gmail.com
--000e0cd29c467aa7410489b6b73b-- From owner-chemistry@ccl.net Thu Jun 24 09:35:01 2010 From: "rocky walden rocky.walden19~!~gmail.com" To: CCL Subject: CCL: Help needed in interpretation of NMR chemical sheilding values calculated using Computational Tool (TURBOMOLE) Message-Id: <-42162-100624005938-15872-BQ/xCAGGsAXh5EV8/Ilonw===server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=0016e64605782932590489bf85e0 Date: Thu, 24 Jun 2010 10:29:32 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19{:}gmail.com] --0016e64605782932590489bf85e0 Content-Type: text/plain; charset=ISO-8859-1 Hi All, I have recently downloaded the latest version of turbomole and started working on it. I used Hartree-Fock method i have optimized the geometry of the molecule and next after optimization i have asked the application to Calculate NMR chemical shielding values. I job was success ful and i got a human readble file as an output, which has the anisotropic and isotropic , values. The values i got were different form the experimental. My molecule is simple Acetaldehyde. I cant find any value which is nearly matching to my experimental value. Is there any other calculation that i need to perform on my NMR chemical shield out put values which simplifes and gives results in delta values ( where experimental values are represented ). Looking forward for your help. Regards walden R --0016e64605782932590489bf85e0 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,
=A0I have recently downloaded the latest version of turbomole an= d started working on it.
=A0I used Hartree-Fock method i have optimized = the geometry of the molecule and next after optimization i have asked the a= pplication to Calculate NMR chemical shielding values.
=A0I job was success ful and i got a human readble file as an output, which= has the anisotropic and isotropic , values.
=A0The values i got were di= fferent form the experimental.
=A0My molecule is=A0 simple Acetaldehyde.=
=A0I cant find any value which is nearly matching to my experimental value.=
=A0
=A0Is there any other calculation that i need to perform on my N= MR chemical shield out put values which simplifes and gives results in delt= a values ( where experimental values are represented ).
=A0
Looking forward for your help.
=A0
=A0
Regards
walden R --0016e64605782932590489bf85e0-- From owner-chemistry@ccl.net Thu Jun 24 10:10:01 2010 From: "Henry Martinez hmartine+/-gmail.com" To: CCL Subject: CCL: restart calculation Gaussian FREQ / OPT chk file Message-Id: <-42163-100624095051-8944-Lxe+Zo4vUtScjk8dhjAMZg]~[server.ccl.net> X-Original-From: "Henry Martinez" Date: Thu, 24 Jun 2010 09:50:49 -0400 Sent to CCL by: "Henry Martinez" [hmartine]^[gmail.com] Hi, My calculation run out of time, I have the chk file, and I would like to restart it. I was running both OPT and FREQ calculation. However the keywords I found to restart are opt=restart and freq=restart, but I would like to restart the calculation as it was, both opt and freq. Is there anyway to do this? combine the keywords or something like that?, thanks a lot for you help. From owner-chemistry@ccl.net Thu Jun 24 10:55:00 2010 From: "Zsolt Bikadi zsolt.bikadi]=[virtuadrug.com" To: CCL Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42164-100624105407-9417-efWVekov71UsoLxUOfwrGw---server.ccl.net> X-Original-From: "Zsolt Bikadi" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Thu, 24 Jun 2010 16:53:56 +0200 MIME-Version: 1.0 Sent to CCL by: "Zsolt Bikadi" [zsolt.bikadi],[virtuadrug.com] Hello John, 1, you can convert mopac input to some more common format e.g. mol with Babel 2, then the molfile can be converted to png with molconvert (JChem package) 3, the small images can be merged using the ImageMagick Montage so this is three command altogether. Sincerely, Zsolt -- Zsolt Bikadi, PhD DockingServer Team http://www.dockingserver.com ----- Original Message ----- > From: "John McKelvey jmmckel!^!gmail.com" To: "Bikadi, Zsolt " Sent: Thursday, June 24, 2010 14:17 PM Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files > > Sent to CCL by: John McKelvey [jmmckel,gmail.com] > Hello, > > I have about 50 MOPAC input structures I need to get into 2D drawings > for publication, obviously multiple drawings on a page. Any > suggestions how to do this? > > Thanks! > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel\a/gmail.com> > From owner-chemistry@ccl.net Thu Jun 24 11:29:00 2010 From: "Wolf-D. Ihlenfeldt wdi[]xemistry.com" To: CCL Subject: CCL: AW: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42165-100624105929-22080-H/eBGTQl/fxXe3WUD4zPsg^^^server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 24 Jun 2010 16:59:58 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi[a]xemistry.com] John, let me give it a try. The Cactvs toolkit can read MOPAC input files (most of the time at least, this is not an especially stable format), decode Z matrix data into 3D atomic coordinates, get connectivity from it, perform 2D layout and write output in various formats, including, for example, CDX (Chemdraw) or SKC (ISIS/Draw) for putting final touches on the rendering manually. The software is free for academia (www.xemistry.com/academic). Your problem will require the writing of a small processing script. Can you send me one or two sample structures? > -----Ursprüngliche Nachricht----- > Von: owner-chemistry+wdi==xemistry.com],[ccl.net [mailto:owner- > chemistry+wdi==xemistry.com],[ccl.net] Im Auftrag von John McKelvey > jmmckel!^!gmail.com > Gesendet: Donnerstag, 24. Juni 2010 14:17 > An: Ihlenfeldt, Wolf D > Betreff: CCL: Creating publishable 2D drawings from 3D Z-matrix based > input files > > > Sent to CCL by: John McKelvey [jmmckel,gmail.com] > Hello, > > I have about 50 MOPAC input structures I need to get into 2D drawings > for publication, obviously multiple drawings on a page. Any > suggestions how to do this? > > Thanks! > > John > > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel\a/gmail.com > > > From owner-chemistry@ccl.net Thu Jun 24 12:04:00 2010 From: "Jim Kress ccl_nospam]|[kressworks.com" To: CCL Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42166-100624112153-2989-3FvgNqjGV8kYCqwSpvU7Tg^server.ccl.net> X-Original-From: "Jim Kress" Content-Language: en-us Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 24 Jun 2010 11:21:38 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam%a%kressworks.com] mol2mol? http://www.gunda.hu/mol2mol/index.html Jim -----Original Message----- > From: owner-chemistry+ccl_nospam==kressworks.com-$-ccl.net [mailto:owner-chemistry+ccl_nospam==kressworks.com-$-ccl.net] On Behalf Of John McKelvey jmmckel!^!gmail.com Sent: Thursday, June 24, 2010 8:17 AM To: Kress, Jim Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based input files Sent to CCL by: John McKelvey [jmmckel,gmail.com] Hello, I have about 50 MOPAC input structures I need to get into 2D drawings for publication, obviously multiple drawings on a page. Any suggestions how to do this? Thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel\a/gmail.comhttp://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 Jun 24 13:00:01 2010 From: "Serdar Badoglu sbadoglu=gazi.edu.tr" To: CCL Subject: CCL:G: Gaussian upgrade Message-Id: <-42167-100624125850-27305-uWlhDK/N7XS3Dj6BU+iKgQ+*+server.ccl.net> X-Original-From: "Serdar Badoglu" Date: Thu, 24 Jun 2010 12:58:48 -0400 Sent to CCL by: "Serdar Badoglu" [sbadoglu%%gazi.edu.tr] Hi CCL'ers We use Gaussian 03W with GaussView 3. Nowadays we're thinking of upgrading ourself to Gaussian 09W Multiprocessor. I'd like to ask that if you know any compatibility issues between G09W and GV3. May we continue to use GV3 when we upgrade to G09W without problems? Or, should we upgrade also GaussView? Thanks. Serdar Badoglu Gazi University Dept. of Physics From owner-chemistry@ccl.net Thu Jun 24 13:34:00 2010 From: "Rinderspacher, Berend (Cont, ARL/WMRD) berend.rinderspacher(0)us.army.mil" To: CCL Subject: CCL:G: restart calculation Gaussian FREQ / OPT chk file (UNCLASSIFIED) Message-Id: <-42168-100624130116-4876-z8DuPTgYSx8DhEYWAqaO/g]-[server.ccl.net> X-Original-From: "Rinderspacher, Berend (Cont, ARL/WMRD)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 24 Jun 2010 13:01:08 -0400 MIME-Version: 1.0 Sent to CCL by: "Rinderspacher, Berend (Cont, ARL/WMRD)" [berend.rinderspacher a us.army.mil] Classification: UNCLASSIFIED Caveats: NONE Dear Henry, Write a two-part continuation: In the first routing section put opt=restart and then add --Link1-- # freq=restart geom=allcheck guess=read etc. Under the other mandatory input. The Gaussian website gives you more pointers on writing multiple routing section decks. -----Original Message----- > From: owner-chemistry+berend.rinderspacher==us.army.mil-.-ccl.net [mailto:owner-chemistry+berend.rinderspacher==us.army.mil-.-ccl.net] On Behalf Of Henry Martinez hmartine+/-gmail.com Sent: Thursday, June 24, 2010 9:51 AM To: Rinderspacher, Berend (Cont, ARL/WMRD) Subject: CCL: restart calculation Gaussian FREQ / OPT chk file Sent to CCL by: "Henry Martinez" [hmartine]^[gmail.com] Hi, My calculation run out of time, I have the chk file, and I would like to restart it. I was running both OPT and FREQ calculation. However the keywords I found to restart are opt=restart and freq=restart, but I would like to restart the calculation as it was, both opt and freq. Is there anyway to do this? combine the keywords or something like that?, thanks a lot for you help.http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtClassification: UNCLASSIFIED Caveats: NONE From owner-chemistry@ccl.net Thu Jun 24 14:10:00 2010 From: "David Watson dewatson++olemiss.edu" To: CCL Subject: CCL: Help needed in interpretation of NMR chemical sheilding values calculated using Computational Tool (TURBOMOLE) Message-Id: <-42169-100624123218-909-BayH9N9Ifcuu96emNbnQCQ+/-server.ccl.net> X-Original-From: David Watson Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 24 Jun 2010 11:32:10 -0500 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: David Watson [dewatson#olemiss.edu] On Jun 23, 2010, at 11:59 PM, rocky walden rocky.walden19~!~gmail.com wrote: > Hi All, > I have recently downloaded the latest version of turbomole and started working on it. > I used Hartree-Fock method i have optimized the geometry of the molecule and next after optimization i have asked the application to Calculate NMR chemical shielding values. > I job was success ful and i got a human readble file as an output, which has the anisotropic and isotropic , values. > The values i got were different form the experimental. > My molecule is simple Acetaldehyde. > I cant find any value which is nearly matching to my experimental value. > > Is there any other calculation that i need to perform on my NMR chemical shield out put values which simplifes and gives results in delta values ( where experimental values are represented ). > Take a look at JOC 2009, 74, 4597-4607. http://pubs.acs.org/doi/abs/10.1021/jo900408d > Looking forward for your help. > > > Regards > walden R From owner-chemistry@ccl.net Thu Jun 24 14:45:00 2010 From: "Bradley Kenneth Welch bwelch5(!)slu.edu" To: CCL Subject: CCL: Using multiple basis sets in G09 Message-Id: <-42170-100624132813-3591-5bqaEKrINxDhzYpnRCYTgg[]server.ccl.net> X-Original-From: "Bradley Kenneth Welch" Date: Thu, 24 Jun 2010 13:28:12 -0400 Sent to CCL by: "Bradley Kenneth Welch" [bwelch5-,-slu.edu] Good afternoon everyone, I am starting a computational project and I need some technical assistance. I need to set up an input file for an optimisation of a platinum complex. I need to use a basis set to account for the platinum (LanL2DZ specifically), and another to account for N,Cl,O, and C (6-311G). In my G09 input file, how would I set it up to use multiple basis sets? Bradley Welch Undergraduate Department of Chemistry Saint Louis University Monsanto Hall, RM 218 3501 Laclede Ave. St. Louis, Mo 63103-2010 email: bwelch5()slu.edu From owner-chemistry@ccl.net Thu Jun 24 15:19:00 2010 From: "Wolf-D. Ihlenfeldt wdi^_^xemistry.com" To: CCL Subject: CCL: AW: Creating publishable 2D drawings from 3D Z-matrix based input files Message-Id: <-42171-100624131110-18411-Y/CfhuqqNRrwa6girKrkog[#]server.ccl.net> X-Original-From: "Wolf-D. Ihlenfeldt" Content-Language: de Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 24 Jun 2010 19:11:37 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf-D. Ihlenfeldt" [wdi-x-xemistry.com] I do not think mol2mol does 2D layout, which is, if I understood the original posting correctly, the core of the problem... if you just want to render 3D structures, there are lots of other possibilities, besides mol2mol... > -----Ursprüngliche Nachricht----- > Von: owner-chemistry+wdi==xemistry.com-.-ccl.net [mailto:owner- > chemistry+wdi==xemistry.com-.-ccl.net] Im Auftrag von Jim Kress > ccl_nospam]|[kressworks.com > Gesendet: Donnerstag, 24. Juni 2010 17:22 > An: Ihlenfeldt, Wolf D > Betreff: CCL: Creating publishable 2D drawings from 3D Z-matrix based > input files > > > Sent to CCL by: "Jim Kress" [ccl_nospam%a%kressworks.com] > mol2mol? > > http://www.gunda.hu/mol2mol/index.html > > > Jim > > -----Original Message----- > > From: owner-chemistry+ccl_nospam==kressworks.com : ccl.net > [mailto:owner-chemistry+ccl_nospam==kressworks.com : ccl.net] On Behalf > Of > John McKelvey jmmckel!^!gmail.com > Sent: Thursday, June 24, 2010 8:17 AM > To: Kress, Jim > Subject: CCL: Creating publishable 2D drawings from 3D Z-matrix based > input > files > > > Sent to CCL by: John McKelvey [jmmckel,gmail.com] > Hello, > > I have about 50 MOPAC input structures I need to get into 2D drawings > for publication, obviously multiple drawings on a page. Any > suggestions how to do this? > > Thanks! > > John From owner-chemistry@ccl.net Thu Jun 24 15:54:00 2010 From: "Tapas Kar tapas.kar a usu.edu" To: CCL Subject: CCL:G: Using multiple basis sets in G09 Message-Id: <-42172-100624151242-10343-Hn8UzV3N3uiBa2JvLbsOYA(a)server.ccl.net> X-Original-From: Tapas Kar Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 24 Jun 2010 13:12:35 -0600 MIME-Version: 1.0 Sent to CCL by: Tapas Kar [tapas.kar.:.usu.edu] Hello, Please check the Gen & GenECP document at following link. http://www.gaussian.com/g_tech/g_ur/k_gen.htm Thanks Tapas -----Original Message----- > From: owner-chemistry+tapas.kar==usu.edu],[ccl.net [mailto:owner-chemistry+tapas.kar==usu.edu],[ccl.net] On Behalf Of Bradley Kenneth Welch bwelch5(!)slu.edu Sent: Thursday, June 24, 2010 11:28 AM To: Tapas Kar Subject: CCL: Using multiple basis sets in G09 Sent to CCL by: "Bradley Kenneth Welch" [bwelch5-,-slu.edu] Good afternoon everyone, I am starting a computational project and I need some technical assistance. I need to set up an input file for an optimisation of a platinum complex. I need to use a basis set to account for the platinum (LanL2DZ specifically), and another to account for N,Cl,O, and C (6-311G). In my G09 input file, how would I set it up to use multiple basis sets? Bradley Welch Undergraduate Department of Chemistry Saint Louis University Monsanto Hall, RM 218 3501 Laclede Ave. St. Louis, Mo 63103-2010 email: bwelch5#slu.eduhttp://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 Jun 24 16:30:00 2010 From: "Cheri McFerrin cmcfer1[*]tigers.lsu.edu" To: CCL Subject: CCL:G: Using multiple basis sets in G09 Message-Id: <-42173-100624151545-13167-BN0hQIvIHpz6NO4f/akd6A a server.ccl.net> X-Original-From: Cheri McFerrin Content-Type: multipart/alternative; boundary=001636ed78d8b7725d0489cb7ae7 Date: Thu, 24 Jun 2010 14:15:37 -0500 MIME-Version: 1.0 Sent to CCL by: Cheri McFerrin [cmcfer1(_)tigers.lsu.edu] --001636ed78d8b7725d0489cb7ae7 Content-Type: text/plain; charset=ISO-8859-1 bradley: here is an analog-type input for you. *********************************************** %chk=/work/default/cmcfer1/job346.chk %nprocs=8 %mem=20mw #m06/gen opt=(maxcycles=100) freq scf=intrep t 0 9 fe o 1 1.806 o 1 1.806 2 179. h 2 .9675 1 137.5 3 90. h 3 .9675 1 137.5 2 90. o h 0 aug-cc-pvtz **** fe 0 lanl2dz **** all Gaussian input files must terminate w a blank line. ***************************************************************** cheers, cheri mcferrin On Thu, Jun 24, 2010 at 12:28 PM, Bradley Kenneth Welch bwelch5(!)slu.edu < owner-chemistry]-[ccl.net> wrote: > > Sent to CCL by: "Bradley Kenneth Welch" [bwelch5-,-slu.edu] > Good afternoon everyone, > > > I am starting a computational project and I need some technical > assistance. I > need to set up an input file for an optimisation of a platinum complex. I > need > to use a basis set to account for the platinum (LanL2DZ specifically), and > another to account for N,Cl,O, and C (6-311G). In my G09 input file, how > would > I set it up to use multiple basis sets? > > > Bradley Welch > Undergraduate > Department of Chemistry > Saint Louis University > Monsanto Hall, RM 218 > 3501 Laclede Ave. > St. Louis, Mo 63103-2010 > email: bwelch5#slu.edu> > > --001636ed78d8b7725d0489cb7ae7 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable bradley:

here is an analog-type input for you.

***********************************************
<= div>%chk=3D/work/default/cmcfer1/job346.chk
%nprocs=3D8
%mem=3D20mw

#m06/gen opt=3D(maxcycles=3D100) freq = scf=3Dintrep

t

0 9
<= div>fe
o 1 1.806
o 1 1.806 2 179.
h 2 .9675 1= 137.5 3 90.
h 3 .9675 1 137.5 2 90.

o h 0
aug-c= c-pvtz
****
fe 0
lanl2dz
****
=
all Gaussian input files must terminate w a blank line.
*****************************************************************

cheers, cheri mcferrin

= On Thu, Jun 24, 2010 at 12:28 PM, Bradley Kenneth Welch bwelch5(!)slu.edu <owner-chemistry]-[ccl.net> wrote:

Sent to CCL by: "Bradley =A0Kenneth Welch" [bwelch5-,-slu.edu]
Good afternoon everyone,


I am starting a computational project =A0and I need some technical assistan= ce. I
need to set up an input file for an optimisation of a platinum complex. I n= eed
to use a basis set to account for the platinum (LanL2DZ specifically), and<= br> another to account for N,Cl,O, and C (6-311G). In my G09 input file, how wo= uld
I set it up to use multiple basis sets?


Bradley Welch
Undergraduate
Department of Chemistry
Saint Louis University
Monsanto Hall, RM 218
3501 Laclede Ave.
St. Louis, Mo 63103-2010
email: bwelch5#slu.edu



-=3D This is automatically added to each message by the mailing script =3D-=
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--001636ed78d8b7725d0489cb7ae7-- From owner-chemistry@ccl.net Thu Jun 24 17:05:00 2010 From: "David Hose anthrax_brothers]_[hotmail.com" To: CCL Subject: CCL:G: Using multiple basis sets in G09 Message-Id: <-42174-100624162038-14104-Vn635zLIjODI6fSDeFSUIQ{}server.ccl.net> X-Original-From: "David Hose" Date: Thu, 24 Jun 2010 16:20:36 -0400 Sent to CCL by: "David Hose" [anthrax_brothers^^^hotmail.com] Bradley, The online G09 manual shows you how to do this here (see very bottom of the page). http://www.gaussian.com/g_tech/g_ur/k_pseudo.htm # Becke3LYP/Gen Pseudo=Read Opt Test HF/6-31G(d) Opt of Cr(CO)6 0 1 Cr 0.0 0.0 0.0 molecule specification continues C O 0 6-31G(d) **** Cr 0 LANL2DZ **** Cr 0 LANL2DZ Its worth noting that if you are going to be doing any calculations upon molecules that don't have a metal, than the 5D vs 6D issue can arise. Check out the "Additional Basis Set-Related Keywords" and "Issues Arising from Pure vs. Cartesian Basis Functions" on this page of the manual. http://www.gaussian.com/g_tech/g_ur/m_basis_sets.htm If in doubt include 5D in the route section of the input file. Hope that helps. Regards, Dave. ====== Good afternoon everyone, I am starting a computational project and I need some technical assistance. I need to set up an input file for an optimisation of a platinum complex. I need to use a basis set to account for the platinum (LanL2DZ specifically), and another to account for N,Cl,O, and C (6-311G). In my G09 input file, how would I set it up to use multiple basis sets? Bradley Welch Undergraduate Department of Chemistry Saint Louis University Monsanto Hall, RM 218 3501 Laclede Ave. St. Louis, Mo 63103-2010 email: bwelch5#slu.edu From owner-chemistry@ccl.net Thu Jun 24 17:40:00 2010 From: "Jamin Krinsky jamink]^[berkeley.edu" To: CCL Subject: CCL: Using multiple basis sets in G09 Message-Id: <-42175-100624162334-16920-zxcczLYp0krpCIk8gIodMg!=!server.ccl.net> X-Original-From: Jamin Krinsky Content-Type: multipart/alternative; boundary=0016363b7fe22ec1a40489cc6d9c Date: Thu, 24 Jun 2010 13:23:24 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink- -berkeley.edu] --0016363b7fe22ec1a40489cc6d9c Content-Type: text/plain; charset=ISO-8859-1 Dear Bradley, I put together a little primer on that, go to http://glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html and look at the first choice. Regards, Jamin On Thu, Jun 24, 2010 at 10:28 AM, Bradley Kenneth Welch bwelch5(!)slu.edu < owner-chemistry++ccl.net> wrote: > > Sent to CCL by: "Bradley Kenneth Welch" [bwelch5-,-slu.edu] > Good afternoon everyone, > > > I am starting a computational project and I need some technical > assistance. I > need to set up an input file for an optimisation of a platinum complex. I > need > to use a basis set to account for the platinum (LanL2DZ specifically), and > another to account for N,Cl,O, and C (6-311G). In my G09 input file, how > would > I set it up to use multiple basis sets? > > > Bradley Welch > Undergraduate > Department of Chemistry > Saint Louis University > Monsanto Hall, RM 218 > 3501 Laclede Ave. > St. Louis, Mo 63103-2010 > email: bwelch5#slu.edu> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink++berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu --0016363b7fe22ec1a40489cc6d9c Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Bradley,
I put together a little primer on that, go to
http:/= /glab.cchem.berkeley.edu/glab/faqs/gauss_custombasis.html
and look a= t the first choice.
Regards,
Jamin


On Thu, Jun 24, 201= 0 at 10:28 AM, Bradley Kenneth Welch bwelch5(!)s= lu.edu <owner-chemistry++ccl.net> wrote:

Sent to CCL by: "Bradley =A0Kenneth Welch" [bwelch5-,-slu.edu]
Good afternoon everyone,


I am starting a computational project =A0and I need some technical assistan= ce. I
need to set up an input file for an optimisation of a platinum complex. I n= eed
to use a basis set to account for the platinum (LanL2DZ specifically), and<= br> another to account for N,Cl,O, and C (6-311G). In my G09 input file, how wo= uld
I set it up to use multiple basis sets?


Bradley Welch
Undergraduate
Department of Chemistry
Saint Louis University
Monsanto Hall, RM 218
3501 Laclede Ave.
St. Louis, Mo 63103-2010
email: bwelch5#slu.edu



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--
Jamin L Krinsky, Ph.D.<= br>Molecular Graphics and Computation Facility
175 Tan Hall, University = of California, Berkeley, CA 94720
jamink++berkeley.edu, 510-643-0616
http://glab.cchem.berkeley.edu

--0016363b7fe22ec1a40489cc6d9c-- From owner-chemistry@ccl.net Thu Jun 24 18:15:00 2010 From: "Ol Ga eurisco1 ~~ pochta.ru" To: CCL Subject: CCL: Using multiple basis sets in G09 Message-Id: <-42176-100624165522-17988-4uPjc7eEDbVpXaqBgAn7tw]*[server.ccl.net> X-Original-From: "Ol Ga" Date: Thu, 24 Jun 2010 16:55:20 -0400 Sent to CCL by: "Ol Ga" [eurisco1[A]pochta.ru] Dear Bradley Kenneth Welch, An example special for your case: # b3lyp/Gen pseudo=read {additional keywords} comment 0 1 <---- just an example {coordinates} {blank line} C, Cl, O, N 0 6-311g* **** Pt 0 Lanl2DZ **** {blank line} Pt 0 Lanl2DZ Sincerely, Ol Ga -------------------------------------------------- > From: "Bradley Kenneth Welch bwelch5(!)slu.edu" Sent: Thursday, June 24, 2010 9:28 PM To: "Ga, Ol " Subject: CCL: Using multiple basis sets in G09 > > > Sent to CCL by: "Bradley Kenneth Welch" [bwelch5-,-slu.edu] > Good afternoon everyone, > > > I am starting a computational project and I need some technical assistance. I > need to set up an input file for an optimisation of a platinum complex. I need > to use a basis set to account for the platinum (LanL2DZ specifically), and > another to account for N,Cl,O, and C (6-311G). In my G09 input file, how would > I set it up to use multiple basis sets? > > > Bradley Welch > Undergraduate > Department of Chemistry > Saint Louis University > Monsanto Hall, RM 218 > 3501 Laclede Ave. > St. Louis, Mo 63103-2010 > email: bwelch5#slu.edu > > > From owner-chemistry@ccl.net Thu Jun 24 18:49:01 2010 From: "Farhan Pasha pashafa(-)yahoo.co.in" To: CCL Subject: CCL:G: restart calculation Gaussian FREQ / OPT chk file Message-Id: <-42177-100624140338-8968-y2I7zVw8wXujcJUX48OBZA ~ server.ccl.net> X-Original-From: Farhan Pasha Content-Type: multipart/alternative; boundary="0-1721347012-1277402605=:97133" Date: Thu, 24 Jun 2010 23:33:25 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: Farhan Pasha [pashafa[#]yahoo.co.in] --0-1721347012-1277402605=:97133 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi it seems simple just what to do, remove all the coordinates from input file= keep only up to charge and multiplicity and add "geom=3Dcheck" in to keywo= rds line and simply run the calculation. I hope it will work. cheers Correspondence Address =0ADr. Syed Farhan Ahmad Pasha --- On Thu, 24/6/10, Henry Martinez hmartine+/-gmail.com wrote: > From: Henry Martinez hmartine+/-gmail.com Subject: CCL: restart calculation Gaussian FREQ / OPT chk file To: "Pasha, Frahan Ahmad " Date: Thursday, 24 June, 2010, 7:20 PM Sent to CCL by: "Henry=A0 Martinez" [hmartine]^[gmail.com] Hi,=20 My calculation run out of time, I have the chk file, and I would like to re= start it. I was running both OPT=20 and FREQ calculation. However the keywords I found to restart are opt=3Dres= tart and freq=3Drestart, but I=20 would like to restart the calculation as it was, both opt and freq. Is ther= e anyway to do this? combine=20 the keywords or something like that?, thanks a lot for you help. -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A --0-1721347012-1277402605=:97133 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi
it seems simple just what to do, remove= all the coordinates from input file keep only up to charge and multiplicit= y and add "geom=3Dcheck" in to keywords line and simply run the calculation= .
I hope it will work.

cheers

Correspondence Address
= =0ADr. Syed Farhan Ahmad Pasha

--- On Thu, 24/6/10, Henry Martine= z hmartine+/-gmail.com <owner-chemistry . ccl.net> wrote:

From: Henry Martinez hmartine+/-gmail.com <= ;owner-chemistry . ccl.net>
Subject: CCL: restart calculation Gaussian = FREQ / OPT chk file
To: "Pasha, Frahan Ahmad " <pashafa . yahoo= .co.in>
Date: Thursday, 24 June, 2010, 7:20 PM


Sent to CCL by: "Henry  Martinez" [hmartine]^[gmail.com]=
Hi,
My calculation run out of time, I have the chk file, and I woul= d like to restart it. I was running both OPT
and FREQ calculation. Howe= ver the keywords I found to restart are opt=3Drestart and freq=3Drestart, b= ut I
would like to restart the calculation as it was, both opt and freq= . Is there anyway to do this? combine
the keywords or something like th= at?, thanks a lot for you help.



-=3D This is automatically added= to each message by the mailing script =3D-
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--0-1721347012-1277402605=:97133-- From owner-chemistry@ccl.net Thu Jun 24 19:24:00 2010 From: "Josh Dibble ddibble:+:uci.edu" To: CCL Subject: CCL:G: Using multiple basis sets in G09 Message-Id: <-42178-100624174715-4672-MKOnjLcvikrgO1t75/TkYQ[*]server.ccl.net> X-Original-From: Josh Dibble Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 24 Jun 2010 14:46:56 -0700 MIME-Version: 1.0 Sent to CCL by: Josh Dibble [ddibble%x%uci.edu] I have multiple basis sets for an nmr simulation I am doing. I use EPR-III for carbon and hydrogen and aug-cc-pVDZ for nitrogen and oxygen. The end of my file looks like so: 46 47 48 C H 0 EPR-III **** N O 0 aug-cc-pVDZ **** Notice the space between the molecular specification and basis set specification. The beginning of the file includes: b3lyp/gen Letting gaussian know to use b3lyp and the basis set specification at the end. cheers, Josh On 6/24/2010 10:28 AM, Bradley Kenneth Welch bwelch5(!)slu.edu wrote: > Sent to CCL by: "Bradley Kenneth Welch" [bwelch5-,-slu.edu] > Good afternoon everyone, > > > I am starting a computational project and I need some technical assistance. I > need to set up an input file for an optimisation of a platinum complex. I need > to use a basis set to account for the platinum (LanL2DZ specifically), and > another to account for N,Cl,O, and C (6-311G). In my G09 input file, how would > I set it up to use multiple basis sets? > > > Bradley Welch > Undergraduate > Department of Chemistry > Saint Louis University > Monsanto Hall, RM 218 > 3501 Laclede Ave. > St. Louis, Mo 63103-2010 > email: bwelch5#slu.edu> > >