From owner-chemistry@ccl.net Tue May 18 01:58:00 2010 From: "Mudit Dixit dixitmuditk++gmail.com" To: CCL Subject: CCL:G: GAMESS GUI -- suggestions? Message-Id: <-41879-100517155425-25594-te7fFhUSIj947bS90MeKBQ]=[server.ccl.net> X-Original-From: Mudit Dixit Content-Type: multipart/alternative; boundary=0016e6d7ef6278abb80486cf1632 Date: Tue, 18 May 2010 00:48:19 +0530 MIME-Version: 1.0 Sent to CCL by: Mudit Dixit [dixitmuditk|,|gmail.com] --0016e6d7ef6278abb80486cf1632 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Dr. Jensen Avogadro (http://avogadro.openmolecules.net/wiki/Main_Page) will be helpful to you . It has an Gamess(even for Gaussian ) input generator. It is avilable in both Win/Linux Go to Extension>Gamess> input generator With Best Regards, Mudit Dixit JRF c/o Dr. Saurav Pal Physical Chemistry Division, ESTG, NCL PUNE,INDIA Ext:2298 Ph: +91-9762174017 On Mon, May 17, 2010 at 9:11 AM, Roy Jensen JensenRH:MacEwan.ca < owner-chemistry],[ccl.net> wrote: > > Sent to CCL by: Roy Jensen [JensenRH[a]MacEwan.ca] > All > > I am new to GAMESS (very familiar with Gaussian) and will be teaching > an undergraduate course this fall using GAMESS. I am looking for > recommendations on a _functional_ and _user friendly_ GUI for GAMESS. > The GUI must be able to write input files and interpret output files. > > Thanks, > Dr. Roy Jensen > (=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D)-----------------------------------------= =A4 > Chemistry, Grant MacEwan University > Room 5-172J, 10700-104 Avenue > Edmonton, AB T5J 4S2 > 780.633.3915 > > > > - This is automatically added to each message by the mailing script -> > > --0016e6d7ef6278abb80486cf1632 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Dr.=A0 Jensen

Avogadro (http://avogadro.openmolecules.net/wiki/M= ain_Page) will be helpful to you . It has an Gamess(even for Gaussian )= input generator. It is avilable in both Win/Linux
Go to Extension>Gamess>=A0 input generator

With Best Regards,=

Mudit Dixit
JRF
c/o Dr. Saurav Pal
Physical Chemistry Divi= sion,
ESTG,
NCL PUNE,INDIA
Ext:2298
Ph: +91-9762174017 =A0 =A0 = =A0 =A0


On Mon, May 17, 2010 at 9:11 AM, Roy Jen= sen JensenRH:MacEwan.ca <owner-chemistry],[ccl.net> wrote:

Sent to CCL by: Roy Jensen [JensenRH[a]MacEwan.ca]
All

I am new to GAMESS (very familiar with Gaussian) and will be teaching
an undergraduate course this fall using GAMESS. I am looking for
recommendations on a _functional_ and _user friendly_ GUI for GAMESS.
The GUI must be able to write input files and interpret output files.

Thanks,
=A0Dr. Roy Jensen
(=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D)-----------------------------------------= =A4
=A0Chemistry, Grant MacEwan University
=A0Room 5-172J, 10700-104 Avenue
=A0Edmonton, AB =A0 =A0T5J 4S2
=A0780.633.3915



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--0016e6d7ef6278abb80486cf1632-- From owner-chemistry@ccl.net Tue May 18 08:49:00 2010 From: "Rebecca Wade rebecca.wade() h-its.org" To: CCL Subject: CCL: BDBDB2: Biological Diffusion and Brownian Dynamics Brainstorm 2 Message-Id: <-41880-100518025911-22607-tMzFEfjrpd8pX5/cyyFrpg__server.ccl.net> X-Original-From: "Rebecca Wade" Date: Tue, 18 May 2010 02:59:09 -0400 Sent to CCL by: "Rebecca Wade" [rebecca.wade ~ h-its.org] You are cordially invited to the second Biological Diffusion and Brownian Dynamics Brainstorm. which will take place on October 11-13, 2010. The goal of this workshop is to provide a forum for intensive discussions about the state-of-the-art in Brownian Dynamics simulations of biological macromolecules and related methodologies. Particular attention will be paid to the theoretical description of concentrated media, simulations in cell-like environments and in-vivo measurements of diffusion. Participants will include theoreticians and experimentalists. Speakers will be encouraged to present work in progress and discuss speculative ideas. Topics include: molecular diffusion, Diffusional association, Hydrodynamic interactions, Aggregation, oligomerization, and self-assembly, Macromolecular crowding, Macromolecular flexibility The meeting will take place at the Villa Bosch, Heidelberg, Germany, and, via video-conferencing, at the University of California, San Diego (UCSD). There will be live video-conferencing sessions each evening (Heidelberg)/morning (San Diego). Further information and registration can be found on our website: http://projects.villa-bosch.de/mcm/BDBDB2/ The deadline for registration and submitting abstracts is August 31, 2010. Organizers: Paolo Mereghetti & Rebecca Wade (Heidelberg Institute for Theoretical Studies (HITS), Heidelberg) Contact: bdbdb=-=h-its.org Mark Twain: "One thinks Heidelberg by day--with its surroundings-- is the last possibility of the beautiful; but when he sees Heidelberg by night, a fallen Milky Way, with that glittering railway constellation pinned to the border, he requires time to consider upon the verdict.". From 'A Tramp Abroad'. http://twain.thefreelibrary.com/Tramp-Abroad/0-2 From owner-chemistry@ccl.net Tue May 18 09:24:00 2010 From: "Jan H Jensen jhjensen++kemi.ku.dk" To: CCL Subject: CCL: GAMESS GUI - suggestions Message-Id: <-41881-100518035731-1962-dV52eDtOJryM05l2RRF0Xw : server.ccl.net> X-Original-From: "Jan H Jensen" Date: Tue, 18 May 2010 03:57:30 -0400 Sent to CCL by: "Jan H Jensen" [jhjensen]-[kemi.ku.dk] I use 3 programs (all are open source and run on Mac, Windows, and Linux): Avogadro for the molecule building and GAMESS input file generation http://avogadro.openmolecules.net/wiki/Main_Page GAMESSQ for running the GAMESS job http://www.msg.chem.iastate.edu/GAMESS/GamessQ/ MacMolPlt for extracting data from the GAMESS log file http://www.scl.ameslab.gov/MacMolPlt/ You can see a screencast of how I do it here: http://molecularmodelingbasics.blogspot.com/2009/07/typical-set-of-gamess-calculations.html Other GAMESS related posts: http://molecularmodelingbasics.blogspot.com/search/label/gamess Other Avogradro related posts: http://molecularmodelingbasics.blogspot.com/search/label/avogadro Other MacMolPlt related posts: http://molecularmodelingbasics.blogspot.com/search/label/macmolplt Hope this helps. Best regards, Jan Jensen From owner-chemistry@ccl.net Tue May 18 09:59:00 2010 From: "Visvaldas K. coyote_v2002!A!yahoo.com" To: CCL Subject: CCL: Hints for computer purchasing Message-Id: <-41882-100518014816-11071-o2me5X82r6JwgOxWqD42tA- -server.ccl.net> X-Original-From: "Visvaldas K." Content-Type: text/plain; charset=us-ascii Date: Mon, 17 May 2010 22:48:07 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Visvaldas K." [coyote_v2002#,#yahoo.com] I would just add that big cache size (the bigger the better) *really* speeds up the code compiled using "optimize" flags. Vis From owner-chemistry@ccl.net Tue May 18 13:28:01 2010 From: "partha kundu partha1kundu() yahoo.com" To: CCL Subject: CCL:G: GAR2PED Message-Id: <-41883-100518132636-9302-026wGHB4ObVExPEw18/13Q[a]server.ccl.net> X-Original-From: partha kundu Content-Type: multipart/alternative; boundary="0-1109901839-1274203584=:30546" Date: Tue, 18 May 2010 22:56:24 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: partha kundu [partha1kundu%a%yahoo.com] --0-1109901839-1274203584=:30546 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear all, According to your suggestions I add=A0 ./ at the beginning to run GAR2PED. = Also I add path "export PATH=3D/path/to/gar2ped\:$PATH". Now it is saying= =20 bash: ./pullarc: No such file or directory. Is it that GAR2PED is not compatible with the output of the G03W? Do I need= to do something in Gaussian to make it compatible. Please help. Thanks in advance. Partha.=20 --- On Sun, 16/5/10, zborowsk#chemia.uj.edu.pl wr= ote: > From: zborowsk#chemia.uj.edu.pl Subject: CCL: GAR2PED To: "Kundu, Partha Pratim " Date: Sunday, 16 May, 2010, 2:21 PM Sent to CCL by: zborowsk^^chemia.uj.edu.pl > > Sent to CCL by: "partha=A0 kundu" [partha1kundu+*+yahoo.com] > Dear all, > I have installed GAR2PED software in my computer. According to the readme > file I am typing the command pullarc . But it is saying=A0 "-ba= sh: > pullarc: command not found". Please suggest me what to do. in order to execute program in linux/unix you must to add ./ at the beginni= ng in your case ./pullarc And check if the status of the pullarc file is enable executing, if not change this using the chmod command > Thanks in advance. > Partha.> > > --=20 Krzysztof K. Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax:=A0 +48(12)634-05-15 email: zborowsk=3Dchemia.uj.edu.pl gg 3817259 skype kzys70 www.chemia.uj.edu.pl/~zborowsk -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A --0-1109901839-1274203584=:30546 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear all,
According to your suggestions I = add  ./ at the beginning to run GAR2PED. Also I add path "export PATH= =3D/path/to/gar2ped\:$PATH". Now it is saying
bash: ./pullarc: No such = file or directory.
Is it that GAR2PED is not compatible with the output = of the G03W? Do I need to do something in Gaussian to make it compatible.Please help.
Thanks in advance.
Partha.

--- On Sun, 16/5= /10, zborowsk#chemia.uj.edu.pl <owner-chemistry+/-ccl.net> w= rote:

From: zborowsk#chemia.uj.edu.pl <o= wner-chemistry+/-ccl.net>
Subject: CCL: GAR2PED
To: "Kundu, Partha P= ratim " <partha1kundu+/-yahoo.com>
Date: Sunday, 16 May, 201= 0, 2:21 PM


Sent to CCL by: zborowsk^^chemia.uj.edu.pl

>
> Sent to CCL by: "partha&nbs= p; kundu" [partha1kundu+*+yahoo.com]
> Dear all,
> I have insta= lled GAR2PED software in my computer. According to the readme
> file = I am typing the command pullarc <filename>. But it is saying  "-= bash:
> pullarc: command not found". Please suggest me what to do.
in order to execute program in linux/unix you must to add ./ at the be= ginning
in your case ./pullarc

And check if the status of the pul= larc file is enable executing, if not
change this using the chmod comman= d




> Thanks in advance.
> Partha.>
>>


--
Krzysztof K. Zborowski
Faculty of Chemistry
J= agiellonian University
3 Ingardena Street
30-060 Krakow
Poland
= phone: +48(12)632-4888 ext. 2064 or 2067
fax:  +48(12)634-05-15
= email: zborowsk=3Dchemia.uj.edu.pl
gg 3817259
skype kzys70
www.chemia.uj.edu.pl/~zborowsk



-=3D This is autom= atically added to each message by the mailing script =3D-
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--0-1109901839-1274203584=:30546-- From owner-chemistry@ccl.net Tue May 18 14:05:00 2010 From: "Grigoriy Zhurko reg_zhurko|*|chemcraftprog.com" To: CCL Subject: CCL:G: GAMESS GUI -- suggestions? Message-Id: <-41884-100518124550-12355-+KPFZiRA9fP0qSCOfS6bQw__server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Date: Tue, 18 May 2010 19:51:13 -0700 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko{=}chemcraftprog.com] Helo, > Sent to CCL by: Soren Eustis [soreneustis .. gmail.com] > I am partial to chemcraft (chemcraftprog.org) > Soren The chemcraftprog.org domain is obsolete. You can download the latest ver= sion of the program at chemcraftprog.com domain. Grigoriy Zhurko. > On 17.05.2010, at 05:41, "Roy Jensen JensenRH:MacEwan.ca" > wrote: >> Sent to CCL by: Roy Jensen [JensenRH[a]MacEwan.ca] >> All >> I am new to GAMESS (very familiar with Gaussian) and will be teaching >> an undergraduate course this fall using GAMESS. I am looking for >> recommendations on a _functional_ and _user friendly_ GUI for GAMESS. >> The GUI must be able to write input files and interpret output files. >> Thanks, >> Dr. Roy Jensen >> (=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D)----------------------------------------= -=C2=A4 >> Chemistry, Grant MacEwan University >> Room 5-172J, 10700-104 Avenue >> Edmonton, AB T5J 4S2 >> 780.633.3915 >> - This is automatically added to each message by the mailing script =3D- >> To recover the email address of the author of the message, please =20 >> change> Conferences: http://server.ccl.net/chemistry/announcements/=20 >> conferences/> From owner-chemistry@ccl.net Tue May 18 15:15:00 2010 From: "zborowsk _ chemia.uj.edu.pl" To: CCL Subject: CCL:G: GAR2PED Message-Id: <-41885-100518151414-29276-75ebEpd6uPUe0w/xVHY//g*server.ccl.net> X-Original-From: zborowsk%chemia.uj.edu.pl Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-2 Date: Tue, 18 May 2010 21:14:02 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: zborowsk]_[chemia.uj.edu.pl > Dear all, > According to your suggestions I add  ./ at the beginning to run GAR2PED. > Also I add path "export PATH=/path/to/gar2ped\:$PATH". Now it is saying > bash: ./pullarc: No such file or directory. > Is it that GAR2PED is not compatible with the output of the G03W? Do I > need to do something in Gaussian to make it compatible. > Please help. > Thanks in advance. > Partha. Yes, this is a kind of incompatibility, probably in general, with any windowa version. If I remember well you must change in the archive of the windows gaussian output all "\" (backslash) into "/" (slash). I hope this help Kzys > > --- On Sun, 16/5/10, zborowsk#chemia.uj.edu.pl > wrote: > >> From: zborowsk#chemia.uj.edu.pl > Subject: CCL: GAR2PED > To: "Kundu, Partha Pratim " > Date: Sunday, 16 May, 2010, 2:21 PM > > > Sent to CCL by: zborowsk^^chemia.uj.edu.pl > >> >> Sent to CCL by: "partha  kundu" [partha1kundu+*+yahoo.com] >> Dear all, >> I have installed GAR2PED software in my computer. According to the >> readme >> file I am typing the command pullarc . But it is saying  >> "-bash: >> pullarc: command not found". Please suggest me what to do. > > in order to execute program in linux/unix you must to add ./ at the > beginning > in your case ./pullarc > > And check if the status of the pullarc file is enable executing, if not > change this using the chmod command > > > > >> Thanks in advance. >> Partha.> >> >> > > > -- > Krzysztof K. Zborowski > Faculty of Chemistry > Jagiellonian University > 3 Ingardena Street > 30-060 Krakow > Poland > phone: +48(12)632-4888 ext. 2064 or 2067 > fax:  +48(12)634-05-15 > email: zborowsk=chemia.uj.edu.pl > gg 3817259 > skype kzys70 > www.chemia.uj.edu.pl/~zborowsk    >       >            > > -- Krzysztof K. Zborowski Faculty of Chemistry Jagiellonian University 3 Ingardena Street 30-060 Krakow Poland phone: +48(12)632-4888 ext. 2064 or 2067 fax: +48(12)634-05-15 email: zborowsk{=}chemia.uj.edu.pl gg 3817259 skype kzys70 www.chemia.uj.edu.pl/~zborowsk From owner-chemistry@ccl.net Tue May 18 15:50:00 2010 From: "David Watson dewatson!^!olemiss.edu" To: CCL Subject: CCL:G: GAR2PED Message-Id: <-41886-100518150007-15614-EfSnuIES4i4+8Elo/U4gZg ~~ server.ccl.net> X-Original-From: David Watson Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Tue, 18 May 2010 13:59:55 -0500 Mime-Version: 1.0 (Apple Message framework v1078) Sent to CCL by: David Watson [dewatson*o*olemiss.edu] On May 18, 2010, at 12:26 PM, partha kundu partha1kundu() yahoo.com = wrote: > Dear all, > According to your suggestions I add ./ at the beginning to run = GAR2PED. Also I add path "export PATH=3D/path/to/gar2ped\:$PATH". Now it = is saying=20 > bash: ./pullarc: No such file or directory. > Is it that GAR2PED is not compatible with the output of the G03W? Do I = need to do something in Gaussian to make it compatible. > Please help. No, that's not what that error means. That particular error (i.e. "No such file or directory") means that you = didn't set your path correctly. You may want to try something more like export PATH=3D/path/to/gar2ped:$PATH but this really depends on which shell you are using. When you type echo $PATH you should see something like: /path/to/gar2ped:/bin:/usr/bin ... If you don't see /path/to/gar2ped (or whatever directory you put gar2ped = in), then you still haven't set it up correctly. > Thanks in advance. > Partha.=20 >=20 > --- On Sun, 16/5/10, zborowsk#chemia.uj.edu.pl = wrote: >=20 > From: zborowsk#chemia.uj.edu.pl > Subject: CCL: GAR2PED > To: "Kundu, Partha Pratim " > Date: Sunday, 16 May, 2010, 2:21 PM >=20 >=20 > Sent to CCL by: zborowsk^^chemia.uj.edu.pl >=20 > > > > Sent to CCL by: "partha kundu" [partha1kundu+*+yahoo.com] > > Dear all, > > I have installed GAR2PED software in my computer. According to the = readme > > file I am typing the command pullarc . But it is saying = "-bash: > > pullarc: command not found". Please suggest me what to do. >=20 > in order to execute program in linux/unix you must to add ./ at the = beginning > in your case ./pullarc >=20 > And check if the status of the pullarc file is enable executing, if = not > change this using the chmod command >=20 >=20 >=20 >=20 > > Thanks in advance. > > Partha.> > > > > >=20 >=20 > --=20 > Krzysztof K. Zborowski > Faculty of Chemistry > Jagiellonian University > 3 Ingardena Street > 30-060 Krakow > Poland > phone: +48(12)632-4888 ext. 2064 or 2067 > fax: +48(12)634-05-15 > email: zborowsk=3Dchemia.uj.edu.pl > gg 3817259 > skype kzys70 > www.chemia.uj.edu.pl/~zborowsk >=20 >=20 >=20 > -=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 line to the {:} sign. You can also>=20 > E-mail to subscribers: CHEMISTRY{:}ccl.net or use:>=20 > E-mail to administrators: CHEMISTRY-REQUEST{:}ccl.net or use>=20 > Subscribe/Unsubscribe:=20>=20>=20 > Job: http://www.ccl.net/jobs=20 > Conferences: = http://server.ccl.net/chemistry/announcements/conferences/ >=20>=20 >=20>=20>=20 >=20 >=20 From owner-chemistry@ccl.net Tue May 18 16:24:00 2010 From: "Brian Salter-Duke brian.james.duke : gmail.com" To: CCL Subject: CCL:G: GAR2PED Message-Id: <-41887-100518145156-10433-BZ3ZruyQLjACxJ1vDIoyRw-*-server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Tue, 18 May 2010 19:22:27 +0100 MIME-Version: 1.0 Sent to CCL by: Brian Salter-Duke [brian.james.duke-x-gmail.com] On Tue, May 18, 2010 at 10:56:24PM +0530, partha kundu partha1kundu() yahoo.com wrote: > Dear all, > According to your suggestions I add  ./ at the beginning to run GAR2PED. Also I add path "export PATH=/path/to/gar2ped\:$PATH". Now it is saying > bash: ./pullarc: No such file or directory. The ./ says pullarc is in the current directory. It clearly is not. If you really do have /path/to/gar2ped on your path, just typing "gar2ped" at the prompt should work. I suggest you try typing just /path/to/gar2ped at the prompt. If that does not work, then the error is in gar2ped. It that a compiled program or is it a script. Your original error may be somethign about a line in gar2ped, not that it can not find gar2ped. Brian. > Is it that GAR2PED is not compatible with the output of the G03W? Do I need to do something in Gaussian to make it compatible. > Please help. > Thanks in advance. > Partha. > > --- On Sun, 16/5/10, zborowsk#chemia.uj.edu.pl wrote: > > > From: zborowsk#chemia.uj.edu.pl > Subject: CCL: GAR2PED > To: "Kundu, Partha Pratim " > Date: Sunday, 16 May, 2010, 2:21 PM > > > Sent to CCL by: zborowsk^^chemia.uj.edu.pl > > > > > Sent to CCL by: "partha  kundu" [partha1kundu+*+yahoo.com] > > Dear all, > > I have installed GAR2PED software in my computer. According to the readme > > file I am typing the command pullarc . But it is saying  "-bash: > > pullarc: command not found". Please suggest me what to do. > > in order to execute program in linux/unix you must to add ./ at the beginning > in your case ./pullarc > > And check if the status of the pullarc file is enable executing, if not > change this using the chmod command > > > > > > Thanks in advance. > > Partha.> > > > > > > > -- > Krzysztof K. Zborowski > Faculty of Chemistry > Jagiellonian University > 3 Ingardena Street > 30-060 Krakow > Poland > phone: +48(12)632-4888 ext. 2064 or 2067 > fax:  +48(12)634-05-15 > email: zborowsk=chemia.uj.edu.pl > gg 3817259 > skype kzys70 > www.chemia.uj.edu.pl/~zborowsk          >            > -- Brian Salter-Duke (Brian Duke) 626 Melbourne Rd, Spotswood, VIC, 3015, Australia. Email: b_duke^_^bigbond.net.au Phone: 03-93992847 Web: http://www.salter-duke.bigpondhosting.com/brian/index.htm From owner-chemistry@ccl.net Tue May 18 17:05:00 2010 From: "Venable, Richard (NIH/NHLBI) E venabler||nhlbi.nih.gov" To: CCL Subject: CCL:G: GAR2PED Message-Id: <-41888-100518165550-3133-Hwtzp9arFQVv2fPgmL5xAw^server.ccl.net> X-Original-From: "Venable, Richard (NIH/NHLBI) [E]" Content-Language: en Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 18 May 2010 16:53:26 -0400 MIME-Version: 1.0 Sent to CCL by: "Venable, Richard (NIH/NHLBI) [E]" [venabler[#]nhlbi.nih.gov] A few basic Linux/Unix things to note here-- [1] the ./ prefix is *only* correct when the executable program is in the c= urrent working directory, so that was probably misleading advice; I suggest= removing the ./ prefix [2] the string "/path/to" must be replaced by the actual full pathname on y= our system; change to the directory where the program resides, and type the= command pwd The string returned is the full path, which should replace "/path/to" in th= e example given. -- Rick Venable 5635 FL/T906 Membrane Biophysics Section NIH/NHLBI Lab. of Computational Biology Bethesda, MD 20892-9314 U.S.A. (301) 496-1905 venabler AT nhlbi*nih*gov On 5/18/10 1:26 PM, "Barry Hardy barry.hardy*o*vtxmail.ch" wrote: Dear all, According to your suggestions I add ./ at the beginning to run GAR2PED. Al= so I add path "export PATH=3D/path/to/gar2ped\:$PATH". Now it is saying bash: ./pullarc: No such file or directory. Is it that GAR2PED is not compatible with the output of the G03W? Do I need= to do something in Gaussian to make it compatible. Please help. Thanks in advance. Partha. --- On Sun, 16/5/10, zborowsk#chemia.uj.edu.pl = wrote: > From: zborowsk#chemia.uj.edu.pl Subject: CCL: GAR2PED To: "Kundu, Partha Pratim " Date: Sunday, 16 May, 2010, 2:21 PM Sent to CCL by: zborowsk^^chemia.uj.edu.pl > > Sent to CCL by: "partha kundu" [partha1kundu+*+yahoo.com] > Dear all, > I have installed GAR2PED software in my computer. According to the readme > file I am typing the command pullarc . But it is saying "-bash= : > pullarc: command not found". Please suggest me what to do. in order to execute program in linux/unix you must to add ./ at the beginni= ng in your case ./pullarc And check if the status of the pullarc file is enable executing, if not change this using the chmod command From owner-chemistry@ccl.net Tue May 18 20:43:00 2010 From: "Alex M Clark aclark.xyz(_)gmail.com" To: CCL Subject: CCL: Mobile Molecular DataSheet v1.0.0 released Message-Id: <-41889-100518190025-7764-K2SIUHMYfUainovWkMegDg .. server.ccl.net> X-Original-From: "Alex M Clark" Date: Tue, 18 May 2010 19:00:24 -0400 Sent to CCL by: "Alex M Clark" [aclark.xyz_-_gmail.com] Dear CCL, For anybody who is interested in chemistry software for mobile devices, there is a new app available for BlackBerry smartphones called the Mobile Molecular DataSheet. Its most striking feature is a molecular diagram sketcher which is optimised for the small screen/trackball/keypad interface. It also allows groups of molecules to be organised along with text and numeric data, which can be edited using a spreadsheet-like interface. Standard data formats (MDL MOL & SD) can be imported, exported and exchanged by email. For more information, see the webside for Molecular Materials Informatics, at: http://www.molmatinf.com There are also a number of demo videos which are available via youtube, such as: http://www.youtube.com/watch?v=lqYXUNk6Gmw All comments and inquiries are welcome. Best regards, Alex. From owner-chemistry@ccl.net Tue May 18 21:18:00 2010 From: "Richard Harper drrwharper!^!gmail.com" To: CCL Subject: CCL: Library enumeration software Message-Id: <-41890-100518171829-21716-GXd3g6YL4eMYhySJiD8v4Q,+,server.ccl.net> X-Original-From: Richard Harper Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 18 May 2010 16:47:48 -0400 MIME-Version: 1.0 Sent to CCL by: Richard Harper [drrwharper^^^gmail.com] What software are you using to enumerate (virtual or real) libraries of chemicals from a scaffold and sets of reagents? Among the requirements are the ability to enumerate large libraries (10^6 or more compounds); some flexibility in naming (ability to record the identifiers of the reactants); and Open Source or free academic license (or very inexpensive). Any suggestions are appreciated. Dick Harper Indiana University-Purdue University Indianapolis (IUPUI) From owner-chemistry@ccl.net Tue May 18 23:41:00 2010 From: "Neeraj Naithani neerajnaithani^^^gmail.com" To: CCL Subject: CCL: QSPR Software Message-Id: <-41891-100518215707-25794-3NSFZ6+BCRtBysZ7gxY3hw|server.ccl.net> X-Original-From: "Neeraj Naithani" Date: Tue, 18 May 2010 21:57:05 -0400 Sent to CCL by: "Neeraj Naithani" [neerajnaithani=-=gmail.com] can anybody suggest QSPR software for polymeric system. Thank You