From owner-chemistry@ccl.net Fri Oct 13 01:05:01 2006 From: "Daniil Bratashov dn2010-#-gmail.com" To: CCL Subject: CCL: Free molecular builder Message-Id: <-32786-061013003642-29438-RgFewfNKGhfh9gowKwARjQ%server.ccl.net> X-Original-From: Daniil Bratashov Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII Date: Fri, 13 Oct 2006 08:37:27 +0400 Mime-Version: 1.0 Sent to CCL by: Daniil Bratashov [dn2010*o*gmail.com] On Thu, 12 Oct 2006 12:12:21 -0400 "Sherin Alfalah shireen.alfalah{:}yahoo.com" wrote: > I am wondering if there is a free and practical molecular builder > that runs on Windows linux platforms. It would be very nice if there > is one that runs on both platforms at the same time. ccp1gui, ghemical and openbabel to convert files. WBR, Daniil Bratashov. From owner-chemistry@ccl.net Fri Oct 13 03:52:00 2006 From: "Shireen Falah shireen.alfalah|yahoo.com" To: CCL Subject: CCL: more on free molecular builder Message-Id: <-32787-061013034402-9849-il5EBQOqVw1sT4HuppQ+RQ===server.ccl.net> X-Original-From: Shireen Falah Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-1804146508-1160721837=:16992" Date: Thu, 12 Oct 2006 23:43:57 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Shireen Falah [shireen.alfalah,,yahoo.com] --0-1804146508-1160721837=:16992 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear All, Thank you very much for your kind replies but what I am looking for is a software that I can use to build the molecules from scratch and give out the geometry in a format (such as "xyz" or "z-matrix") which i can use to in an input file to run some ab-into calculations on the system of interest. I am aware of molden and molekel but I use them for viewing. I am looking for a software that is free and can funstion partially as "spartan" or "cerius". Best regards, ************************************** Sherin Alfalah PhD Student Theoretical Chemist Chemistry Department AlQuds University ************************************** --------------------------------- Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business. --0-1804146508-1160721837=:16992 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear All,
 
Thank you very much for your kind replies but what I am looking for is a software that I can use to build the molecules from scratch and give out the geometry in a format (such as "xyz" or "z-matrix") which i can use to in an input file to run some ab-into calculations on the system of interest.
I am aware of molden and molekel but I use them for viewing. I am looking for a software that is free and can funstion partially as "spartan" or "cerius".
 
Best regards,
 


**************************************
Sherin Alfalah
PhD Student
Theoretical Chemist
Chemistry Department
AlQuds University
**************************************

Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business. --0-1804146508-1160721837=:16992-- From owner-chemistry@ccl.net Fri Oct 13 05:20:02 2006 From: "Jens Thomas j.m.h.thomas%x%dl.ac.uk" To: CCL Subject: CCL: more on free molecular builder Message-Id: <-32788-061013045819-18796-uqFB7ywyCL0vkFhCEUU11Q[#]server.ccl.net> X-Original-From: Jens Thomas Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 13 Oct 2006 09:57:42 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Thomas [j.m.h.thomas+/-dl.ac.uk] Hi Sherin, The ccp1gui should be able to do what you require. It can build up molecules from scratch and can also construct z-matrices for structures. It's free software and will run on any platform that Python and VTK will build on, which is pretty much most things knocking around today. You can find out more about it at: http://www.cse.clrc.ac.uk/qcg/ccp1gui/index.shtml Please let me know if you have any problems with it. Best wishes, Jens Shireen Falah shireen.alfalah|yahoo.com wrote: > Sent to CCL by: Shireen Falah [shireen.alfalah,,yahoo.com] > --0-1804146508-1160721837=:16992 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Dear All, > > Thank you very much for your kind replies but what I am looking for is a software that I can use to build the molecules from scratch and give out the geometry in a format (such as "xyz" or "z-matrix") which i can use to in an input file to run some ab-into calculations on the system of interest. > I am aware of molden and molekel but I use them for viewing. I am looking for a software that is free and can funstion partially as "spartan" or "cerius". > > Best regards, > > > > ************************************** > Sherin Alfalah > PhD Student > Theoretical Chemist > Chemistry Department > AlQuds University > ************************************** > > --------------------------------- > Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business. > --0-1804146508-1160721837=:16992 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear All,
 
Thank you very much for your kind replies but what I am looking for is a software that I can use to build the molecules from scratch and give out the geometry in a format (such as "xyz" or "z-matrix") which i can use to in an input file to run some ab-into calculations on the system of interest.
I am aware of molden and molekel but I use them for viewing. I am looking for a software that is free and can funstion partially as "spartan" or "cerius".
 
Best regards,
 


**************************************
Sherin Alfalah
PhD Student
Theoretical Chemist
Chemistry Department
AlQuds University
**************************************

> > > >

Get your own >> web address for just $1.99/1st yr. We'll help. > Yahoo! Small Business. >> > > --0-1804146508-1160721837=:16992--> > > > > > From owner-chemistry@ccl.net Fri Oct 13 05:54:02 2006 From: "Masahiko Suenaga alohascc(!)mbox.nc.kyushu-u.ac.jp" To: CCL Subject: CCL: more on molecular builder Message-Id: <-32789-061013053538-14025-H6VlZCK0i7MOy1t2vGiyug- -server.ccl.net> X-Original-From: "Masahiko Suenaga" Date: Fri, 13 Oct 2006 05:35:32 -0400 Sent to CCL by: "Masahiko Suenaga" [alohascc**mbox.nc.kyushu-u.ac.jp] Dear all, Try Facio. http://www1.bbiq.jp/zzzfelis/Facio.html Facio is a molecular builder which works on Windows and Linux. And it's a free ware. Only Fedora Core 4 and Scientific Linux 4.2 are tested for Facio run. But it would work well on other Linux distributions. Masahiko Suenaga, Ph.D. Department of Chemistry, Faculty of Sciences, Kyushu University, Japan From owner-chemistry@ccl.net Fri Oct 13 06:29:01 2006 From: "Masahiko Suenaga alohascc#,#mbox.nc.kyushu-u.ac.jp" To: CCL Subject: CCL: more on free molecular builder Message-Id: <-32790-061013062609-22791-uKWEKcgoaIGbM1wTTtE1xw++server.ccl.net> X-Original-From: "Masahiko Suenaga" Date: Fri, 13 Oct 2006 06:26:05 -0400 Sent to CCL by: "Masahiko Suenaga" [alohascc[A]mbox.nc.kyushu-u.ac.jp] Dear all, Try Facio. http://www1.bbiq.jp/zzzfelis/Facio.html Facio is a molecular builder which works on Windows and Linux. And it's a free ware. Only Fedora Core 4 and Scientific Linux 4.2 are tested for Facio run. But it would work well on other Linux distributions. Masahiko Suenaga, Ph.D. Department of Chemistry, Faculty of Sciences, Kyushu University, Japan From owner-chemistry@ccl.net Fri Oct 13 11:35:01 2006 From: "Mark Thompson mark++arguslab.com" To: CCL Subject: CCL: Free molecular builder Message-Id: <-32791-061012185739-32334-SKFtHg0cfiMWpM46Yk+oGw*server.ccl.net> X-Original-From: Mark Thompson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 12 Oct 2006 15:09:10 -0700 MIME-Version: 1.0 Sent to CCL by: Mark Thompson [mark(~)arguslab.com] ArgusLab 4.0 has a reasonably good builder. It's a little buggier than a commercial product like Discovery Studio, but it's free to everyone. It runs on Windows (www.arguslab.com). Mark Dipesh Risal drisal ~ accelrys.com wrote: > Sent to CCL by: Dipesh Risal [drisal###accelrys.com] > This is a multipart message in MIME format. > --=_alternative 005B5C8388257205_= > Content-Type: text/plain; charset="US-ASCII" > > Hi Shireen, > > The Discovery Studio (DS) Visualizer work on both Windows and Linux and is > available for free to academic and commercial users. I am unsure of what > you mean by "runs on both platforms at the same time" but the DS > Visualizer have identical functionality in the two OS's. > > http://www.accelrys.com/products/downloads/ds_visualizer/ > > Sincerely, > > Dipesh Risal, Ph. D. > Product Manager, Life Sciences > Accelrys, Inc. > 10188 Telesis Court, Suite 100 > San Diego, CA 92121, U.S.A. > Tel: +1 (858) 799 5224, Cell: +1 (858) 414 2702 > Fax: +1 (858) 799 5100 > email: drisal++accelrys.com > http://www.accelrys.com > > Join us at the Accelrys User Meeting & Conference > Nov. 13th-15th - Baltimore, Maryland > http://www.accelrys.com/user_meeting > > > > "Sherin Alfalah shireen.alfalah{:}yahoo.com" > Sent by: owner-chemistry++ccl.net > 10/12/2006 09:17 AM > Please respond to > "CCL Subscribers" > > > To > "Risal, Dipesh " > cc > > Subject > CCL: Free molecular builder > > > > > > > Sent to CCL by: "Sherin Alfalah" [shireen.alfalah . yahoo.com] > Dear CCL users, > > I am wondering if there is a free and practical molecular builder that > runs on Windows linux platforms. It would be very nice if there is one > that runs on both platforms at the same time. > > Thanks in advance. > > Best regards, > Shireen Alfalah > PhD student. > Alquds Universityhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt-- > Click on the link below to report this email as spam > https://www.mailcontrol.com/sr/moL2TEWXkzY07ZOOPazWJnHYmVfN8dceLF0YAs6Cp59vh1F55mpug!WcEM55z!IUTEo5jxyBLkmSiFIPGUjNKzcwpLI0tKIHDAozkamvTBkfurBBVJEmTXXZmNSh4Gx9lP9HGKpdekeI89N3YfGSQV4IkOC9bM3PeTJFDQxGr3VFq0WXKDpAOCpD+LY7wcSH6m5LBCnP!M48L31x9esgO6C8nK3p6uY3 > > > > --=_alternative 005B5C8388257205_= > Content-Type: text/html; charset="US-ASCII" > > >
Hi Shireen, >
>
The Discovery Studio (DS) Visualizer > work on both Windows and Linux and is available for free to academic and > commercial users.  I am unsure of what you mean by "runs > on both platforms at the same time" > but the DS Visualizer have identical functionality in the two OS's. >
>
http://www.accelrys.com/products/downloads/ds_visualizer/ >
>
Sincerely, >
>
Dipesh Risal, Ph. D.
> Product Manager, Life Sciences
> Accelrys, Inc.
> 10188 Telesis Court, Suite 100
> San Diego, CA 92121, U.S.A.
> Tel:  +1 (858) 799 5224, Cell:  +1 (858) 414 2702
> Fax: +1 (858) 799 5100
> email: drisal++accelrys.com
> http://www.accelrys.com
>
> Join us at the Accelrys User Meeting & Conference
> Nov. 13th-15th - Baltimore, Maryland
> http://www.accelrys.com/user_meeting >
>
>
> > >
"Sherin Alfalah shireen.alfalah{:}yahoo.com" > <owner-chemistry++ccl.net> >
Sent by: owner-chemistry++ccl.net >

10/12/2006 09:17 AM > > >
>
Please respond to
> "CCL Subscribers" <chemistry++ccl.net>
>
>

> > > > >
>
To
> 		"Risal, Dipesh " <drisal++accelrys.com> >
>
cc
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Subject
> 		CCL: Free molecular builder
>
> > >
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>
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Sent to CCL by: "Sherin  Alfalah" [shireen.alfalah > . yahoo.com]
> Dear CCL users,
>
> I am wondering if there is a free and practical molecular builder that > runs on Windows linux platforms. It would be very nice if there is one > that runs on both platforms at the same time.
>
> Thanks in advance.
>
> Best regards,
> Shireen Alfalah
> PhD student.
> Alquds University
>
>
> > >      http://www.ccl.net/cgi-bin/ccl/send_ccl_message
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> --=_alternative 005B5C8388257205_=--> > > > > > > -- ************************************ Mark Thompson Planaria Software LLC http://www.arguslab.com mark#%#arguslab.com ************************************ From owner-chemistry@ccl.net Fri Oct 13 12:10:00 2006 From: "Shireen Al Falah shireenfalah _ hotmail.com" To: CCL Subject: CCL: more on free molecular builder Message-Id: <-32792-061013102343-555-UGWA7olcgIvsdBin7CwE4Q*server.ccl.net> X-Original-From: "Shireen Al Falah" Content-Type: text/html; format=flowed Date: Fri, 13 Oct 2006 16:23:30 +0200 Mime-Version: 1.0 Sent to CCL by: "Shireen Al Falah" [shireenfalah,,hotmail.com]

Hi,

I think it is just a molecular viewer. I mean you need to have a file in some format so as to transfer it into another format but it can not build the molecule from scratch.

shireen

From:  "Masahiko Suenaga alohascc#,#mbox.nc.kyushu-u.ac.jp" <owner-chemistry^ccl.net>
Reply-To:  "CCL Subscribers" <chemistry^ccl.net>
To:  "Alfalah, Sherin " <shireenfalah^hotmail.com>
Subject:  CCL: more on free molecular builder
Date:  Fri, 13 Oct 2006 06:33:20 -0400
>Sent to CCL by: "Masahiko  Suenaga" [alohascc[A]mbox.nc.kyushu-u.ac.jp]
>Dear all,
>
>Try Facio.
>http://www1.bbiq.jp/zzzfelis/Facio.html
>
>Facio is a molecular builder which works on
>Windows and Linux. And it's a free ware.
>
>Only Fedora Core 4 and Scientific Linux 4.2 are
>tested for Facio run. But it would work well on
>other Linux distributions.
>
>
>Masahiko Suenaga, Ph.D.
>Department of Chemistry,
>Faculty of Sciences,
>Kyushu University, Japan
>
>
>
>
>
>
>
>
>
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MSN Messenger overalt med WebMessenger From owner-chemistry@ccl.net Fri Oct 13 12:45:00 2006 From: "Crowther, Robert L robert_l.crowther ~ roche.com" To: CCL Subject: CCL: more on free molecular builder Message-Id: <-32793-061013102716-1349-pWuOQY6hNzcEJYDSBVGa7g]-[server.ccl.net> X-Original-From: "Crowther, Robert L" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Oct 2006 09:48:01 -0400 MIME-Version: 1.0 Sent to CCL by: "Crowther, Robert L" [robert_l.crowther-$-roche.com] Maybe check out Arguslab? It's free. I know it runs on Windows. Not sure about linux/unix. It can make small molecules from scratch and do a certain amount of minimization. It can also deal with proteins, i.e, it can read in a pdb file. I don't know what kind of output formats are available, but I would be surprized if xyz (at least) wasn't one of them. You can check it out at http://www.planaria-software.com/ Someone-somewhere-once wrote a gui interface to MOPAC that built molecules for you and then set up the MOPAC script. I don't know if it is still available anymore. MOPAC itself is available for free at http://openmopac.net/ but MOPAC is just the geometry/energy minimization part of the problem. I think someone has already suggested Facio. Haven't tried it, but it looks to be mostly a visualization program, not a builder. It can be found at http://www1.bbiq.jp/zzzfelis/Facio.html You may be able to get by with the free version of Chemsketch, depending on how much you may (or may not) need the builder/visualizer to do for you. You can certainly build even complex molecules (buckyballs or cyclic peptides, for example) and dump them out as mdl.mol files, but the output formats available is severely restricted in the non-commercial version. You can check out Chemsketch at http://www.acdlabs.com/download/chemsk.html There is also a free version of ISISdraw, which is similar to Chemsketch. Check out http://www.mdli.com/solutions/solutions_for/academics/ and look at the "no fee" section somewhere in the middle of the page. Hopefully, one of those will work for you. None of the free builders/visualizers is all that much of a molecular mechanics program--Arguslab comes the closest in my opinion--so the idea would be to build in one program and do the "real" energy computations in MOPAC or something similar. Arguslab has MM2/MM3 capability. Maybe they've added more by now. But Arguslab won't be as reliable or complete as something like cerius--but it will be a *lot* cheaper. -----Original Message----- > From: owner-chemistry]^[ccl.net [mailto:owner-chemistry]^[ccl.net] Sent: Friday, October 13, 2006 4:04 AM To: Crowther, Robert L {DISC~Nutley} Subject: CCL: more on free molecular builder Sent to CCL by: Shireen Falah [shireen.alfalah,,yahoo.com] --0-1804146508-1160721837=:16992 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Dear All, Thank you very much for your kind replies but what I am looking for is a software that I can use to build the molecules from scratch and give out the geometry in a format (such as "xyz" or "z-matrix") which i can use to in an input file to run some ab-into calculations on the system of interest. I am aware of molden and molekel but I use them for viewing. I am looking for a software that is free and can funstion partially as "spartan" or "cerius". Best regards, ************************************** Sherin Alfalah PhD Student Theoretical Chemist Chemistry Department AlQuds University ************************************** --------------------------------- Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business. --0-1804146508-1160721837=:16992 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Dear All,
 
Thank you very much for your kind replies but what I am looking for is a software that I can use to build the molecules from scratch and give out the geometry in a format (such as "xyz" or "z-matrix") which i can use to in an input file to run some ab-into calculations on the system of interest.
I am aware of molden and molekel but I use them for viewing. I am looking for a software that is free and can funstion partially as "spartan" or "cerius".
 
Best regards,
 


**************************************
Sherin Alfalah
PhD Student
Theoretical Chemist
Chemistry Department
AlQuds University
**************************************

Get your own web address for just $1.99/1st yr. We'll help. Yahoo! Small Business. --0-1804146508-1160721837=:16992--http://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 Fri Oct 13 13:19:00 2006 From: "Jim Kress ccl_nospam^^^kressworks.com" To: CCL Subject: CCL: more on free molecular builder Message-Id: <-32794-061013121942-5209-HYHZRGfObjHfO1rGHD1xFQ:_:server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Oct 2006 12:14:30 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam * kressworks.com] ChemCraft http://www.chemcraftprog.com Or ArgusLab http://www.arguslab.com Will do what you want. In particular, Chemcraft contains an automatic symmetry analyzer and allows you to construct z-matrix output. Jim > -----Original Message----- > From: Shireen Falah shireen.alfalah|yahoo.com > [mailto:owner-chemistry#,#ccl.net] > Sent: Friday, October 13, 2006 3:58 AM > To: Kress, Jim > Subject: CCL: more on free molecular builder > > Sent to CCL by: Shireen Falah [shireen.alfalah,,yahoo.com] > --0-1804146508-1160721837=:16992 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Dear All, > > Thank you very much for your kind replies but what I am > looking for is a software that I can use to build the > molecules from scratch and give out the geometry in a format > (such as "xyz" or "z-matrix") which i can use to in an input > file to run some ab-into calculations on the system of interest. > I am aware of molden and molekel but I use them for > viewing. I am looking for a software that is free and can > funstion partially as "spartan" or "cerius". > > Best regards, > > > > ************************************** > Sherin Alfalah > PhD Student > Theoretical Chemist > Chemistry Department > AlQuds University > ************************************** > > --------------------------------- > Get your own web address for just $1.99/1st yr. We'll help. > Yahoo! Small Business. > --0-1804146508-1160721837=:16992 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear All,
 
Thank > you very much for your kind replies but what I am > looking for is a software that I can use to build the > molecules from scratch and give out the geometry in a format > (such as "xyz" or "z-matrix") which i can use to in an input > file to run some ab-into calculations on the system of > interest.
I am aware of molden and molekel but I > use them for viewing. I am looking for a software that is > free and can funstion partially as "spartan" or "cerius". >
 
Best regards,
>
 


************************************* > *
Sherin Alfalah
PhD Student
Theoretical Chemist >
Chemistry Department
AlQuds University >
**************************************

> > > >

Get your own >web address for just $1.99/1st yr. We'll help. href="http://us.rd.yahoo.com/evt=41244/*http://smallbusiness.y > ahoo.com/" > >Yahoo! Small Business. > > --0-1804146508-1160721837=:16992-- > > > > -= 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 look up the X-Original-From: line > in the mail header.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From owner-chemistry@ccl.net Fri Oct 13 13:55:00 2006 From: "Jim Kress ccl_nospam(0)kressworks.com" To: CCL Subject: CCL: more on free molecular builder Message-Id: <-32795-061013123021-13376-IU9ZkcLrzp95hCIFqGXzZw]_[server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Fri, 13 Oct 2006 12:30:05 -0400 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam() kressworks.com] Just a helpful hint. CCL is a plain text list (at least for many of us) so when you send a message as HTML it is basically unreadable. Try just sending plain text and you may get a more comprehensive response. Jim > -----Original Message----- > From: Shireen Al Falah shireenfalah _ hotmail.com > [mailto:owner-chemistry!^!ccl.net] > Sent: Friday, October 13, 2006 12:14 PM > To: Kress, Jim > Subject: CCL: more on free molecular builder > > Sent to CCL by: "Shireen Al Falah" > [shireenfalah,,hotmail.com]
style='background-color:'>

Hi,

I > think it is just a molecular viewer. I mean you need to have > a file in some format so as to transfer it into another > format but it can not build the molecule from scratch. >

shireen

style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: > #a0c6e5 2px solid; MARGIN-RIGHT: 0px">
> >
From:  "Masahiko Suenaga > alohascc#,#mbox.nc.kyushu-u.ac.jp" > <owner-chemistry(!)ccl.net>
Reply-To:   > "CCL Subscribers" > <chemistry(!)ccl.net>
To:  "Alfalah, > Sherin " > <shireenfalah(!)hotmail.com>
Subject:   > CCL: more on free molecular > builder
Date:  Fri, 13 Oct 2006 06:33:20 > -0400
>Sent to CCL by: > "Masahiko  Suenaga" > [alohascc[A]mbox.nc.kyushu-u.ac.jp]
>Dear > all,
>
>Try > Facio.
>http://www1.bbiq.jp/zzzfelis/Facio.html
>< > BR>>Facio is a molecular builder which works > on
>Windows and Linux. And it's a free > ware.
>
>Only Fedora Core 4 and Scientific Linux > 4.2 are
>tested for Facio run. But it would work well > on
>other Linux > distributions.
>
>
>Masahiko Suenaga, > Ph.D.
>Department of Chemistry,
>Faculty of > Sciences,
>Kyushu University, > Japan
>
>
>
>
>
>
>< > BR>>
>
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>      
& > gt;
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> MSN Messenger overalt med href="http://g.msn.com/8HMAENNO/2737??PS=47575" > target="_top">WebMessenger > > > > -= 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/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > From owner-chemistry@ccl.net Fri Oct 13 14:30:00 2006 From: "Elaine Chan 06900535r*_*polyu.edu.hk" To: CCL Subject: CCL:G: request for force field parameter change in gaussian03 Message-Id: <-32796-061012224908-10545-Z3YsMKx9al9LrbT6vUfupQ-#-server.ccl.net> X-Original-From: "Elaine Chan" <06900535r- -polyu.edu.hk> Date: Thu, 12 Oct 2006 22:49:07 -0400 Sent to CCL by: "Elaine Chan" [06900535r[-]polyu.edu.hk] I want to use molecular mechanics (force field parameters) of gaussian 03 to optimize platinium complex with toxin substance. But, I don't know how to create the input file of molecualr mechanics. What parameters and force field parameters should be set up? Elaine Chan E-mail: 06900535r:+:polyu.edu.hk From owner-chemistry@ccl.net Fri Oct 13 15:41:00 2006 From: "Kim Branson kim.branson*gmail.com" To: CCL Subject: CCL: more on free molecular builder Message-Id: <-32797-061013050809-27169-JGj5HfGv+yLniDk1Dz+23g%a%server.ccl.net> X-Original-From: Kim Branson Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Fri, 13 Oct 2006 01:30:54 -0700 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: Kim Branson [kim.branson|gmail.com] Ghemical will do what you need. It is free and runs on linux, windows and osx. http://ghemical.ki.ku.dk/wiki/Ghemical there are binaries for each arch. and one can build and minimise in the tripos FF before interfacing with gamess etc. cheers Kim On Oct 13, 2006, at 1:05 AM, Shireen Falah shireen.alfalah|yahoo.com wrote: > Sent to CCL by: Shireen Falah [shireen.alfalah,,yahoo.com] > --0-1804146508-1160721837=:16992 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Dear All, > > Thank you very much for your kind replies but what I am looking > for is a software that I can use to build the molecules from > scratch and give out the geometry in a format (such as "xyz" or "z- > matrix") which i can use to in an input file to run some ab-into > calculations on the system of interest. > I am aware of molden and molekel but I use them for viewing. I am > looking for a software that is free and can funstion partially as > "spartan" or "cerius". > > Best regards, > > > > ************************************** > Sherin Alfalah > PhD Student > Theoretical Chemist > Chemistry Department > AlQuds University > ************************************** > > --------------------------------- > Get your own web address for just $1.99/1st yr. We'll help. Yahoo! > Small Business. > --0-1804146508-1160721837=:16992 > Content-Type: text/html; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > >
Dear All,
 
Thank you very > much for your kind replies but what I am looking for is a software > that I can use to build the molecules from scratch and give out the > geometry in a format (such as "xyz" or "z-matrix") which i can use > to in an input file to run some ab-into calculations on the system > of interest.
I am aware of molden and molekel but I > use them for viewing. I am looking for a software that is free and > can funstion partially as "spartan" or "cerius".
>
 
Best regards,
  DIV>

**************************************
Sherin > Alfalah
PhD Student
Theoretical Chemist
Chemistry > Department
AlQuds University >
**************************************

> > > >

Get your own > web address for just $1.99/1st yr. We'll help. > Yahoo! Small Business. > > --0-1804146508-1160721837=:16992-- > > > > -= 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/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > > From owner-chemistry@ccl.net Fri Oct 13 16:53:00 2006 From: "Praveen Depa praveen_depa . yahoo.com" To: CCL Subject: CCL: Mesoscale Simulation Message-Id: <-32798-061013132702-18904-/kftxhU/CjB0ACoR5KYaOQ[-]server.ccl.net> X-Original-From: Praveen Depa Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Fri, 13 Oct 2006 09:26:52 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Praveen Depa [praveen_depa .. yahoo.com] Arnab, The replacing of a monomer or part of a monomer with a bead is done to extend length and time scales in molecular simulations. This is called coarse-graining in polymer literature. By doing this, you are neglecting some of the degree of freedom which results in loss of information at smaller scales. But you are gaining in computational time. In your case benzene motion abt the axis of polymer is lost if you treat the whole ring to be a coarse-grained bead. If you are specifically interested in benzene ring rotation then you have use more detailed description of the chain. The missing atoms in coarse-grained structure can be reintroduced such that the resulting atomistic chains are at their lowest energy configuration. More details can be found in the literature by searching for 'remapping methods' and 'Kremer et al' (I think). -Praveen. --- "R.Arnab r.arnab]|[gmail.com" wrote: > Sent to CCL by: "R.Arnab" [r.arnab%a%gmail.com] > Hi, > I am planning to do mesoscale simulation of a > polymer system. From > what i understood that the monomer or part of the > monomer is represented > as beads to do tha calculation. What i am little > confused is 'if i chose > a benzene ring to be a bead in a rod like polymer > then during mesoscale > dynamics how it takes care of the rotation of the > ring around the axis > of the rod. And this question also leads to the next > one for the same > reason i.e how to convert the beads to the atomistic > model again.' I > could not find these details as such anywhere and > would appreciate any > reference or inputs in this matter. > > Thanks > Arnab > > > > -= 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 [a] > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST[a]ccl.net > or use> > Before posting, check wait time at: > http://www.ccl.net> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: > ccl, Password: search) > > If your mail bounces from CCL with 5.7.1 error, > check:> > RTFI: > http://www.ccl.net/chemistry/aboutccl/instructions/> > > > __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com