From owner-chemistry@ccl.net Sun Jan 5 09:31:00 2014 From: "Mi yang agri_chemist**yahoo.com" To: CCL Subject: CCL:G: Need help please for Installing G09 on red hat linux Message-Id: <-49510-140105092741-31571-yrntrnPzbGvwmBwj34pxVA-x-server.ccl.net> X-Original-From: "Mi yang" Date: Sun, 5 Jan 2014 09:27:39 -0500 Sent to CCL by: "Mi yang" [agri_chemist,,yahoo.com] Dear CCL colleagues, Happy new year! We are trying to install g09 on red hat linux but could not succeeded. Although Gaussian helpline can help us to some extend, I preferred to consult our best platform CCL. 2. We have made a directory for installation as /usr/local/gaussian and then unpack the g09 inside this directory 3. After ./bsd/install script, there should be some output from installation script but after executing the command ./bsd/install we did not get any output response and neither get any error message for command. What would be the possible reason for not running the./bsd/install script? 4. After execution of installation script, I have tried to run test calculation that has given error that g09 command was not found. 5. I have completed the first 5 steps and I want to know about the 6th step from the following link which say to modify.login or .profile files? Is there really need to make any changes in these files or to create my_login file? Thanks in advance!!! Dr.Mi From owner-chemistry@ccl.net Sun Jan 5 14:50:00 2014 From: "Wang Jian jian.wang],[inbox.com" To: CCL Subject: CCL: Flexible small molecule alignment software Message-Id: <-49511-140104171809-3968-DirA09aeh+G0dAgpzKU8yA\a/server.ccl.net> X-Original-From: Wang Jian Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=US-ASCII Date: Sat, 4 Jan 2014 14:18:02 -0800 Mime-Version: 1.0 Sent to CCL by: Wang Jian [jian.wang]_[inbox.com] <=21DOCTYPE HTML PUBLIC =22-//W3C//DTD HTML 4.0 Transitional//EN=22>
Hi, Michel

That's great=21 Thanks a = lot=21

Jian 


-----Original = Message-----
From: owner-chemistry=40ccl.net
Sent: = Fri, 3 Jan 2014 18:23:10 +0100
To: = jian.wang=40inbox.com
Subject: CCL: Flexible small molecule = alignment software

Hi,

Please have a look at = my softwares/freewares web page (URL below):
* To align rigid = conformers of the same molecule, look at ARMS and POSE.
* To = align rigid conformers of different molecules, look at CSR.
* To align non rigid conformers, select =22representative=22 = conformers of the molecule then do a rigid alignment. =
* To select =22representative=22 = conformers of a molecule, generate an excess of conformers with some = conformer generator (e.g. Frog2 or else) then extract the = =22representative=22 ones with DIVCF.

Happy New Year = =21

Michel.

Michel = Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene = Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral%%gmail.com= (preferred),
        michel.petitjea= n%%univ-paris-diderot.fr
= http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html
=

2014/1/3 Wang Jian jian.wang=5E-=5Einbox.com <owner-chemistry%%ccl.net>
Sent to CCL by: Wang Jian =5Bjian.wang_._inbox.com=5D
Hi, happy new year=21
Can anyone recommend some free software for = conformation analysis and flexible alignment of ligands onto a bioactive = conformation of reference (or template) molecule?
I have some = information such as ChemAxon, FieldAlign, etc. And I want to find = more. 
Thanks in = advance=21

Jian
=
3D=223D
Free 3D Marine Aquarium = Screensaver
Watch dolphins, sharks & orcas on your desktop=21 = Check it out at www.inbox.com/marineaquari= um
From owner-chemistry@ccl.net Sun Jan 5 16:20:00 2014 From: "shanawersi shanawersi=-=upatras.gr" To: CCL Subject: CCL:G: Need help please for Installing G09 on red hat linux Message-Id: <-49512-140105161736-15580-zNYixfYX+kSpa3irxhVIAQ . server.ccl.net> X-Original-From: shanawersi Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Sun, 05 Jan 2014 23:17:23 +0200 MIME-Version: 1.0 Sent to CCL by: shanawersi [shanawersi]-[upatras.gr] Dear Dr Mi I believe you just have to manage path properly to bash and that's it. First of all unpack all modules and files under installation directory "g09" instead of "gaussian". So you will have then path "/usr/local/g09" instead of "/usr/local/gaussian". OK fair enough. Now your installation directory path is "/usr/local/g09" then you can add/save following path in bash file for .profile commands (which i usually use, just copy and paste!!): g09root="/usr/local" GAUSS_SCRDIR="/scratch/g09" export g09root GAUSS_SCRDIR . $g09root/g09/bsd/g09.profile That's all. Now run test job file. I hope it will work with $ g09 input.gjf input.out . One more thing, just check read/write permissions :) Enjoy!!! S. Niaz Greece On 2014-01-05 16:27, Mi yang agri_chemist**yahoo.com wrote: > Sent to CCL by: "Mi yang" [agri_chemist,,yahoo.com] > Dear CCL colleagues, > Happy new year! > We are trying to install g09 on red hat linux but could not > succeeded. > Although Gaussian helpline can > help us to some extend, I preferred to consult our best platform CCL. > 2. We have made a directory for installation as /usr/local/gaussian > and > then unpack the g09 inside this > directory > 3. After ./bsd/install script, there should be some output from > installation script but after executing > the command ./bsd/install we did not get any output response and > neither > get any error message for > command. > What would be the possible reason for not running the./bsd/install > script? > > 4. After execution of installation script, I have tried to run test > calculation that has given error that g09 > command was not found. > 5. I have completed the first 5 steps and I want to know about the > 6th > step from the following link > which say to modify.login or .profile files? > Is there really need to make any changes in these files or to create > my_login file? > > Thanks in advance!!! > > Dr.Mi > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change[1][1][2][3][4] > Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > [5]> [6][7][8] Links: ------ [1][2][3] http://www.ccl.net [4] http://www.ccl.net/jobs [5] http://server.ccl.net/chemistry/announcements/conferences/ [6] http://www.ccl.net/chemistry/searchccl/index.shtml [7][8] http://www.ccl.net/chemistry/aboutccl/instructions/ From owner-chemistry@ccl.net Sun Jan 5 16:55:01 2014 From: "Mikko Vainio mikko.vainio[#]abo.fi" To: CCL Subject: CCL: Flexible small molecule alignment software Message-Id: <-49513-140105152651-27173-DMRhehuD5J41tA861Usb5Q]^[server.ccl.net> X-Original-From: Mikko Vainio Content-Type: multipart/alternative; boundary="------------050408040608030605060003" Date: Sun, 05 Jan 2014 22:26:38 +0200 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio[#]abo.fi] This is a multi-part message in MIME format. --------------050408040608030605060003 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Jian, You may want to try out the following tools as well: http://users.abo.fi/mivainio/balloon/ (conformer generation) http://users.abo.fi/mivainio/shaep/ (aligment) Happy New Year, Mikko On 5.1.2014 0:18, Wang Jian jian.wang],[inbox.com wrote: > Sent to CCL by: Wang Jian [jian.wang]_[inbox.com] > Hi, Michel > > That's great! Thanks a lot! > > Jian > > > -----Original Message----- > *From:* owner-chemistry*ccl.net > *Sent:* Fri, 3 Jan 2014 18:23:10 +0100 > *To:* jian.wang*inbox.com > *Subject:* CCL: Flexible small molecule alignment software > > Hi, > > Please have a look at my softwares/freewares web page (URL below): > * To align rigid conformers of the same molecule, look at ARMS and > POSE. > * To align rigid conformers of different molecules, look at CSR. > * To align non rigid conformers, select "representative" > conformers of the molecule then do a rigid alignment. > * To select "representative" conformers of a molecule, generate an > excess of conformers with some conformer generator (e.g. Frog2 or > else) then extract the "representative" ones with DIVCF. > > Happy New Year ! > > Michel. > > Michel Petitjean > MTi, INSERM UMR-S 973, University Paris 7, > 35 rue Helene Brion, 75205 Paris Cedex 13, France. > Phone: +331 5727 8434; Fax: +331 5727 8372 > E-mail: petitjean.chiral%%gmail.com > (preferred), > michel.petitjean%%univ-paris-diderot.fr > > http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html > > 2014/1/3 Wang Jian jian.wang^-^inbox.com > > > > Sent to CCL by: Wang Jian [jian.wang_._inbox.com > ] > Hi, happy new year! > Can anyone recommend some free software for conformation > analysis and flexible alignment of ligands onto a bioactive > conformation of reference (or template) molecule? > I have some information such as ChemAxon, FieldAlign, etc. And > I want to find more. > Thanks in advance! > > Jian > > ------------------------------------------------------------------------ > --------------050408040608030605060003 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit
Hi Jian,

You may want to try out the following tools as well:
http://users.abo.fi/mivainio/balloon/ (conformer generation)
http://users.abo.fi/mivainio/shaep/ (aligment)

Happy New Year,
Mikko

On 5.1.2014 0:18, Wang Jian jian.wang],[inbox.com wrote:
Sent to CCL by: Wang Jian [jian.wang]_[inbox.com]
Hi, Michel

That's great! Thanks a lot!

Jian 


-----Original Message-----
From: owner-chemistry*ccl.net
Sent: Fri, 3 Jan 2014 18:23:10 +0100
To: jian.wang*inbox.com
Subject: CCL: Flexible small molecule alignment software

Hi,

Please have a look at my softwares/freewares web page (URL below):
* To align rigid conformers of the same molecule, look at ARMS and POSE.
* To align rigid conformers of different molecules, look at CSR.
* To align non rigid conformers, select "representative" conformers of the molecule then do a rigid alignment.
* To select "representative" conformers of a molecule, generate an excess of conformers with some conformer generator (e.g. Frog2 or else) then extract the "representative" ones with DIVCF.

Happy New Year !

Michel.

Michel Petitjean
MTi, INSERM UMR-S 973, University Paris 7,
35 rue Helene Brion, 75205 Paris Cedex 13, France.
Phone: +331 5727 8434; Fax: +331 5727 8372
E-mail: petitjean.chiral%%gmail.com (preferred),
        michel.petitjean%%univ-paris-diderot.fr
http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html

2014/1/3 Wang Jian jian.wang^-^inbox.com <owner-chemistry%%ccl.net>
Sent to CCL by: Wang Jian [jian.wang_._inbox.com]
Hi, happy new year!
Can anyone recommend some free software for conformation analysis and flexible alignment of ligands onto a bioactive conformation of reference (or template) molecule?
I have some information such as ChemAxon, FieldAlign, etc. And I want to find more. 
Thanks in advance!

Jian


--------------050408040608030605060003-- From owner-chemistry@ccl.net Sun Jan 5 17:30:01 2014 From: "John Keller jwkeller#,#alaska.edu" To: CCL Subject: CCL:G: Need help please for Installing G09 on red hat linux Message-Id: <-49514-140105163025-20212-yCtv2GRFdSwm5XUeXA4y+A=-=server.ccl.net> X-Original-From: John Keller Content-Type: multipart/alternative; boundary=001a11369d705744d404ef3fd9ca Date: Sun, 5 Jan 2014 16:30:15 -0500 MIME-Version: 1.0 Sent to CCL by: John Keller [jwkeller-x-alaska.edu] --001a11369d705744d404ef3fd9ca Content-Type: text/plain; charset=ISO-8859-1 Hi, I always use the directions on the WebMO website: http://www.webmo.net/support/binaries_linux.html look under Gaussian 09 section. John Keller On Sun, Jan 5, 2014 at 9:27 AM, Mi yang agri_chemist**yahoo.com < owner-chemistry%%ccl.net> wrote: > > Sent to CCL by: "Mi yang" [agri_chemist,,yahoo.com] > Dear CCL colleagues, > Happy new year! > We are trying to install g09 on red hat linux but could not succeeded. > Although Gaussian helpline can > help us to some extend, I preferred to consult our best platform CCL. > 2. We have made a directory for installation as /usr/local/gaussian and > then unpack the g09 inside this > directory > 3. After ./bsd/install script, there should be some output from > installation script but after executing > the command ./bsd/install we did not get any output response and neither > get any error message for > command. > What would be the possible reason for not running the./bsd/install script? > > 4. After execution of installation script, I have tried to run test > calculation that has given error that g09 > command was not found. > 5. I have completed the first 5 steps and I want to know about the 6th > step from the following link > which say to modify.login or .profile files? > Is there really need to make any changes in these files or to create > my_login file? > > Thanks in advance!!! > > > Dr.Mi> > > --001a11369d705744d404ef3fd9ca Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
I always use the directions on the WebMO website:<= /div>
look under G= aussian 09 section.
John Keller


<= br>
On Sun, Jan 5, 2014 at 9:27 AM, Mi yang agri_= chemist**yahoo.com <<= a href=3D"mailto:owner-chemistry%%ccl.net" target=3D"_blank">owner-chemistry= %%ccl.net> wrote:

Sent to CCL by: "Mi =A0yang" [agri_chemist,,yahoo.com]
Dear CCL colleagues,
Happy new year!
We are trying to install g09 on red hat linux but could not succeeded. Alth= ough Gaussian helpline can
help us to some extend, I preferred to consult our best platform CCL.
2. We have made a directory for installation as /usr/local/gaussian and the= n unpack the g09 inside this
directory
3. After ./bsd/install script, there should be some output from installatio= n script but after executing
the command ./bsd/install we did not get any output response and neither ge= t any error message for
command.
What would be the possible reason for not running the./bsd/install script?<= br>
4. After execution of installation script, I have tried to run test calcula= tion that has given error that g09
command was not found.
5. I have completed the first 5 steps and I want to know about the 6th step= from the following link
which say to modify.login or .profile files?
Is there really need to make any changes in these files or to create my_log= in file?

Thanks in advance!!!


Dr.Mi



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