From owner-chemistry@ccl.net Sun Feb 6 06:44:00 2011 From: "ehsan shakerzadeh ehsan_shakerzadeh!=!yahoo.com" To: CCL Subject: CCL: installation Message-Id: <-43878-110206063104-3210-wBzRzJXyANFlptQ3dmwg1g(~)server.ccl.net> X-Original-From: "ehsan shakerzadeh" Date: Sun, 6 Feb 2011 06:31:02 -0500 Sent to CCL by: "ehsan shakerzadeh" [ehsan_shakerzadeh!^!yahoo.com] Dear All, Is anyone has experience in installation of siesta-2.0.2. I could not install it on Fedora 8. which version is better? I appreciate any one give me details about installation of it. Thank you in advance Ehsan From owner-chemistry@ccl.net Sun Feb 6 07:33:00 2011 From: "Tobias Kraemer tobias.kraemer^^chem.ox.ac.uk" To: CCL Subject: CCL:G: Counterpoise Energy Message-Id: <-43879-110206072848-8390-v4FPVbDUbwMWPbUneHWJ4w|*|server.ccl.net> X-Original-From: Tobias Kraemer Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-15; format=flowed Date: Sun, 06 Feb 2011 12:28:41 +0000 MIME-Version: 1.0 Sent to CCL by: Tobias Kraemer [tobias.kraemer|-|chem.ox.ac.uk] Dear CCL members...... I would appreciate your help with a question that I came across while doing some counterpoise calculations with Gaussian03. In the counterpoise calculation, it turns out that the energy calculated for the dimer in the dimer basis, i.e. E(AB,DCBS), where DCBS is the dimer-centred basis, differs slightly (underestimated by about 0.5 kcal/mol) from the energy obtained from the optimisation of the dimer. These two energies should be the same thing (of course I am using the optimised structure in the counterpoise run), if I have understood the procedure correctly (same geometry, same basis). And apparantly the energies are close, but this result still puzzles me. I consider a difference of up to 0.5 kcal / mol to be rather large, although not really of chemical relevance. I should note that I have used the SCF=tight criterion. Are there other differences between the counterpoise settings in Gaussian and the optimisation, which I have missed? Thanks a lot for your comments Tobias -- _________________________________________ dipl.-chem. tobias krämer department of chemistry inorganic chemistry laboratory university of oxford south parks road oxford OX1 3QR united kingdom |phone| +44 (0)1865 272 135 |email| tobias.kraemer%chem.ox.ac.uk |email| tobias.kraemer%linacre.ox.ac.uk _________________________________________ From owner-chemistry@ccl.net Sun Feb 6 08:22:00 2011 From: "neeraj misra neerajmisra++hotmail.com" To: CCL Subject: CCL: gar2ped Message-Id: <-43880-110206082028-13637-zxPkld6sLH5WPTvgKCowpA_._server.ccl.net> X-Original-From: "neeraj misra" Date: Sun, 6 Feb 2011 08:20:27 -0500 Sent to CCL by: "neeraj misra" [neerajmisra(a)hotmail.com] DEAR MEMBERS, COULD ANYONE TELL ME HOW TO INSTALL GAR2PED PRPGRAM ON FEDORA CORE14..AND HOW TO RUN IT TOO...MY OBJECT IS TO CALCULATE THE POTENTIAL ENERGY DISTRIBUTION.. THANKS From owner-chemistry@ccl.net Sun Feb 6 10:10:01 2011 From: "Jason Swails swails!A!qtp.ufl.edu" To: CCL Subject: CCL: gar2ped Message-Id: <-43881-110206100622-19109-XUQEXHVlfzNF6nv+aLCCkQ]^[server.ccl.net> X-Original-From: Jason Swails Content-Type: multipart/alternative; boundary=90e6ba53a2faf4c0b0049b9e74b1 Date: Sun, 6 Feb 2011 10:06:16 -0500 MIME-Version: 1.0 Sent to CCL by: Jason Swails [swails..:..qtp.ufl.edu] --90e6ba53a2faf4c0b0049b9e74b1 Content-Type: text/plain; charset=ISO-8859-1 Install g77 on your system (gfortran will not work to compile it) and then create a link to g77 called "f77" that is placed somewhere in your PATH. ifort also works to compile gar2ped, so if you have ifort you can create a link to ifort called "f77" somewhere in your path instead. Then just type "make" in the gar2ped directory. (I believe pgf77 would also work if you have that, but I couldn't verify it since I don't have access to it). To use it, look at the README file included in the the source code. Hope this helps, Jason On Sun, Feb 6, 2011 at 8:20 AM, neeraj misra neerajmisra++hotmail.com < owner-chemistry.:.ccl.net> wrote: > > Sent to CCL by: "neeraj misra" [neerajmisra(a)hotmail.com] > DEAR MEMBERS, > COULD ANYONE TELL ME HOW TO INSTALL GAR2PED PRPGRAM ON FEDORA > CORE14..AND HOW TO RUN IT TOO...MY OBJECT IS TO CALCULATE THE POTENTIAL > ENERGY DISTRIBUTION.. > > THANKS> > > -- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Graduate Student 352-392-4032 --90e6ba53a2faf4c0b0049b9e74b1 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Install g77 on your system (gfortran will not work to compile it) and then = create a link to g77 called "f77" that is placed somewhere in you= r PATH.=A0 ifort also works to compile gar2ped, so if you have ifort you ca= n create a link to ifort called "f77" somewhere in your path inst= ead.=A0 Then just type "make" in the gar2ped directory.=A0 (I bel= ieve pgf77 would also work if you have that, but I couldn't verify it s= ince I don't have access to it).

To use it, look at the README file included in the the source code.
=
Hope this helps,
Jason

On Sun, Feb= 6, 2011 at 8:20 AM, neeraj misra neerajmisra++hotmail.com <owner-chemistry.:.ccl.net> wrote:

Sent to CCL by: "neeraj =A0misra" [neerajmisra(a)hotmail.com]
DEAR MEMBERS,
=A0 =A0 =A0 =A0 =A0 =A0 =A0COULD ANYONE TELL ME HOW TO INSTALL GAR2PED PRP= GRAM ON FEDORA CORE14..AND HOW TO RUN IT TOO...MY OBJECT IS TO CALCULATE TH= E POTENTIAL ENERGY DISTRIBUTION..

THANKS



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Jason M. Swails
Quan= tum Theory Project,
University of Florida
Ph.D. Graduate Student
3= 52-392-4032
--90e6ba53a2faf4c0b0049b9e74b1-- From owner-chemistry@ccl.net Sun Feb 6 18:54:00 2011 From: "Adam Tenderholt atenderholt_+_gmail.com" To: CCL Subject: CCL: Geometrical parameters Message-Id: <-43882-110206185027-17256-iy2iebYC1nhQ5dP7TPRPiQ{=}server.ccl.net> X-Original-From: Adam Tenderholt Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 6 Feb 2011 15:50:19 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt---gmail.com] Have you looked at JMol or Jamberoo (http://sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html)? On Wed, Feb 2, 2011 at 11:23 PM, bonoit bonoit bonoit_10(!)yahoo.fr wrote: > > Sent to CCL by: "bonoit  bonoit" [bonoit_10[-]yahoo.fr] > Dear CCLers, > I need a software which is used to set geometrical parameters on a structure to get an image on which we can see the structure (ball and stick) and its geometrical parameters. I try chemoffice but it doesn't work. > Your help will be the most appreciated > Sincerely > bonoit>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/cgi-bin/ccl/send_ccl_message>      http://www.ccl.net/chemistry/sub_unsub.shtml>      http://www.ccl.net/spammers.txt> > > From owner-chemistry@ccl.net Sun Feb 6 19:29:01 2011 From: "Adam Tenderholt atenderholt%a%gmail.com" To: CCL Subject: CCL: Organometallic builder Message-Id: <-43883-110206185315-25523-0NrimKqTNnRhLZi9CperXA ~~ server.ccl.net> X-Original-From: Adam Tenderholt Content-Type: text/plain; charset=ISO-8859-1 Date: Sun, 6 Feb 2011 15:53:07 -0800 MIME-Version: 1.0 Sent to CCL by: Adam Tenderholt [atenderholt[A]gmail.com] Avogadro is pretty good at building molecules. I usually sketch out a structure and then do a quick MM minimization to get a more reasonable structure. On Thu, Feb 3, 2011 at 2:56 PM, Lukman Olawale Olasunkanmi waleolasunkanmi/agmail.com wrote: > Dear All, > Does anyone know of a free molecular builder that is very good at building > organometallic compounds and it is windows compatible? > Thank you > > -- > Olasunkanmi Lukman Olawale > > Department of Chemistry, > Obafemi Awolowo University, > Ile-Ife, Nigeria. > +234-08052401564 > > "Improving our own attitudes and our own state of mind takes time. Haste and > impatience can only defeat our purposes." > > From owner-chemistry@ccl.net Sun Feb 6 20:04:00 2011 From: "Brian Salter-Duke Brian.Salter-Duke/a\monash.edu" To: CCL Subject: CCL:G: gar2ped Message-Id: <-43884-110206170900-10980-JuTdBQlAwEamcQk8duHl8A..server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 7 Feb 2011 09:08:38 +1100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [Brian.Salter-Duke|,|monash.edu] On Sun, Feb 06, 2011 at 10:06:16AM -0500, Jason Swails swails!A!qtp.ufl.edu wrote: > Install g77 on your system (gfortran will not work to compile it) and then > create a link to g77 called "f77" that is placed somewhere in your PATH. > ifort also works to compile gar2ped, so if you have ifort you can create a > link to ifort called "f77" somewhere in your path instead. Then just type > "make" in the gar2ped directory. (I believe pgf77 would also work if you > have that, but I couldn't verify it since I don't have access to it). I was puzzled that gfortran does not work, so I had a look at it. There is an error in the makefile. The first line sets FFLAGS but it is not used, while CFLAGS is used but not set. Change CFLAGS near the bottom to FLAGS. Then I found that setting:- FFLAGS = -std=legacy -fd-lines-as-code gets rid of all errors except one. -std=legacy gets over the non standard do loop in animate. -fd-lines-as-code gets over the objection to lines starting with "D" in column 1. That leaves a problem with format($,' .. in main.f. I just removed the "$,". It then compiles but it does not link. It can not find subroutine filnam. Now I am stuck. Any thoughts. This is very old code and it probably only works for G94. There was a change in format of the coordinates in the output file going from G94 to G98. I got it from CCL and it is dated "13-Dec-1996 12:00". Is there anything more recent? Cheers, Brian. > To use it, look at the README file included in the the source code. > > Hope this helps, > Jason > > On Sun, Feb 6, 2011 at 8:20 AM, neeraj misra neerajmisra++hotmail.com < > owner-chemistry{=}ccl.net> wrote: > > > > > Sent to CCL by: "neeraj misra" [neerajmisra(a)hotmail.com] > > DEAR MEMBERS, > > COULD ANYONE TELL ME HOW TO INSTALL GAR2PED PRPGRAM ON FEDORA > > CORE14..AND HOW TO RUN IT TOO...MY OBJECT IS TO CALCULATE THE POTENTIAL > > ENERGY DISTRIBUTION.. > > > > THANKS> > > > > > > > > > > -- > > Jason M. Swails > > Quantum Theory Project, > > University of Florida > > Ph.D. Graduate Student > > 352-392-4032 -- Brian Salter-Duke (Brian Duke) Brian.Salter-Duke]^[monash.edu Honorary Researcher Fellow Monash Institute of Pharmaceutical Sciences, Monash University Parkville Campus, VIC 3052, Australia. From owner-chemistry@ccl.net Sun Feb 6 23:45:01 2011 From: "sobereva sobjubao]|[yahoo.com.cn" To: CCL Subject: CCL:G: gar2ped Message-Id: <-43885-110206234017-8242-ZGzAr9KFCM6A7pw5+4lSQQ- -server.ccl.net> X-Original-From: sobereva Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 7 Feb 2011 12:40:07 +0800 (CST) MIME-Version: 1.0 Sent to CCL by: sobereva [sobjubao**yahoo.com.cn] Hello, Although gar2ped is an very old software, I found gar2ped still works properly for Gaussian03/09. I've tried compiling gar2ped by gfortran and ifort before but never succeeded. If the operation system you used is not restricted to linux, I suggest you compiling gar2ped by Compaq visual fortran (the version I used is 6.5), I found it is very easy and changing any code is not required. Just build a new project in CVF, drag pullarc.f to project and compile it to pullarc.exe, then clean up the project, drag all other files to project and compile them to gar2ped.exe, Makefile is no use in the compilation. The generated executable files work well. Tian Lu --- On Mon, 2/7/11, Brian Salter-Duke Brian.Salter-Duke/amonash.edu wrote: > From: Brian Salter-Duke Brian.Salter-Duke/amonash.edu > Subject: CCL:G: gar2ped > To: "Lu, Tian " > Date: Monday, February 7, 2011, 6:08 AM > > Sent to CCL by: Brian Salter-Duke > [Brian.Salter-Duke|,|monash.edu] > On Sun, Feb 06, 2011 at 10:06:16AM -0500, Jason Swails > swails!A!qtp.ufl.edu wrote: > > Install g77 on your system (gfortran will not work to > compile it) and then > > create a link to g77 called "f77" that is placed > somewhere in your PATH. > > ifort also works to compile gar2ped, so if you have > ifort you can create a > > link to ifort called "f77" somewhere in your path > instead.  Then just type > > "make" in the gar2ped directory.  (I believe > pgf77 would also work if you > > have that, but I couldn't verify it since I don't have > access to it). > > I was puzzled that gfortran does not work, so I had a look > at it. There > is an error in the makefile. The first line sets FFLAGS but > it is not > used, while CFLAGS is used but not set. Change CFLAGS near > the bottom > to FLAGS. Then I found that setting:- > > FFLAGS = -std=legacy -fd-lines-as-code > > gets rid of all errors except one. -std=legacy gets over > the non > standard do loop in animate. -fd-lines-as-code gets over > the objection > to lines starting with "D" in column 1. That leaves a > problem with > format($,' .. in main.f. I just removed the "$,". It then > compiles but > it does not link. It can not find subroutine filnam. Now I > am stuck. Any > thoughts. > > This is very old code and it probably only works for G94. > There was a > change in format of the coordinates in the output file > going from G94 to > G98. I got it from CCL and it is dated "13-Dec-1996 12:00". > Is there > anything more recent? > > Cheers, Brian. > > > To use it, look at the README file included in the the > source code. > > > > Hope this helps, > > Jason > > > > On Sun, Feb 6, 2011 at 8:20 AM, neeraj misra > neerajmisra++hotmail.com < > > owner-chemistry{=}ccl.net> wrote: > > > > > > > > Sent to CCL by: "neeraj  misra" > [neerajmisra(a)hotmail.com] > > > DEAR MEMBERS, > > >              > COULD ANYONE TELL ME HOW TO INSTALL GAR2PED PRPGRAM ON > FEDORA > > > CORE14..AND HOW TO RUN IT TOO...MY OBJECT IS TO > CALCULATE THE POTENTIAL > > > ENERGY DISTRIBUTION.. > > > > > > THANKS> > > > > > > > > > > > > > > > -- > > > Jason M. Swails > > > Quantum Theory Project, > > > University of Florida > > > Ph.D. Graduate Student > > > 352-392-4032 > > -- >    Brian Salter-Duke (Brian Duke)  > Brian.Salter-Duke:monash.edu >                 >      Honorary Researcher Fellow >             Monash Institute > of Pharmaceutical Sciences, >       Monash University Parkville Campus, > VIC 3052, Australia. > > > > -= 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 >      >      >      > > >