From owner-chemistry@ccl.net Mon Aug 27 01:02:01 2007 From: "Shrinwantu Pal paul/./jncasr.ac.in" To: CCL Subject: CCL: Dihedral angle rotation software Message-Id: <-35029-070827004819-22108-zd5Ei9k+Niz3MufhMLxLzg]_[server.ccl.net> X-Original-From: "Shrinwantu Pal" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 27 Aug 2007 10:25:29 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Shrinwantu Pal" [paul!A!jncasr.ac.in] Dear Milan, I think gauss view can do that with some additional options too. ragards, Shrinwantu Pal JNCASR INDIA From owner-chemistry@ccl.net Mon Aug 27 02:17:00 2007 From: "etamar],[fh.huji.ac.il" To: CCL Subject: CCL:G: NBO CHOOSE keyword Message-Id: <-35030-070827020639-29008-eUwhIUW0Gb+hx+hyANMnlg[a]server.ccl.net> X-Original-From: etamar- -fh.huji.ac.il Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8; DelSp="Yes"; format="flowed" Date: Mon, 27 Aug 2007 08:21:19 +0300 MIME-Version: 1.0 Sent to CCL by: etamar() fh.huji.ac.il HI Which software are you using? If it's Gaussian, than choose doesn't work with g03. Try g98 good luck Tamar Quoting "Pau Farr s pfarras^^icmab.es" : > > Sent to CCL by: "Pau Farr s" [pfarras~~icmab.es] > Hello, > I'm trying to send an NBO calculation from one of my compounds and > there's no way it works. > This is my input: > > NBO 3CBOND END > CHOOSE > lone 1 2 > end > > bond s 1 2 > s 1 3 > s 1 23 > s 1 24 > end > END > > And the error: > NATURAL BOND ORBITAL ANALYSIS: > > Error in input of bond orbitals: > Keyword for orbital type is not LONE, BOND, or 3CBOND (read `1 ') > > I don't want to specify all the lone pairs, bonds and 3cbonds > because my molecule is rather big. I've tried to put only the 3cbond > keyword and I get only 2 units (instead of 10 that I get without > it) but I need only 1 unit, so I'm putting these bonds. > Can someone help me please? > Thanks!> > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Mon Aug 27 05:29:01 2007 From: "Vincent Xianlong Wang xloongw+/-yahoo.com" To: CCL Subject: CCL:G: MFI, zeolite structure with Gaussian03 Message-Id: <-35031-070827052634-19065-lEEf4VG45CD/Bb+ZIspXYQ]-[server.ccl.net> X-Original-From: Vincent Xianlong Wang Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Mon, 27 Aug 2007 02:26:23 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Vincent Xianlong Wang [xloongw||yahoo.com] Hi Jimmy, There is a good source for zeolite structure called Database of Zeolite Structures. Here is the link, http://www.iza-structure.org/databases/. You can download the CIF file of the zeolite from the website and open it in GaussView. Best regards, Vincent --- "Jimmy Lawrence jlawrence%x%slb.com" wrote: > > Sent to CCL by: Jimmy Lawrence [jlawrence{:}slb.com] > Hi CCL members, > > I am a beginner in calculating this type of > system. > Can somebody point a tutorial or share some > experience by simple > instruction on how to build the structure of MFI (or > other zeolite) with > PBC in Gaussian03 (via GaussView) and how to dock > the molecule to > evaluate (e.g. CO2) ? > > Thank you, > > Jimmy > > > > -= 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.> > E-mail to administrators: CHEMISTRY-REQUEST*_*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/> > > > ____________________________________________________________________________________ Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. http://answers.yahoo.com/dir/?link=list&sid=396545469 From owner-chemistry@ccl.net Mon Aug 27 06:55:01 2007 From: "pfarras[]icmab.es" To: CCL Subject: CCL:G: NBO CHOOSE keyword Message-Id: <-35032-070827055127-28568-zd1tvbyWIduBkI3MaOOy5Q(-)server.ccl.net> X-Original-From: pfarras-*-icmab.es Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format="flowed" Date: Mon, 27 Aug 2007 10:53:40 +0200 MIME-Version: 1.0 Sent to CCL by: pfarras===icmab.es Hi! Yes, I'm using g03 and it seems in the manual that it should also work... well, I'll try it with g98. Thank you! Quoting "etamar],[fh.huji.ac.il" : > > Sent to CCL by: etamar() fh.huji.ac.il > HI > Which software are you using? > If it's Gaussian, than choose doesn't work with g03. Try g98 > good luck > Tamar > > Quoting "Pau Farr s pfarras^^icmab.es" : > >> >> Sent to CCL by: "Pau Farr s" [pfarras~~icmab.es] >> Hello, >> I'm trying to send an NBO calculation from one of my compounds and >> there's no way it works. >> This is my input: >> >> NBO 3CBOND END >> CHOOSE >> lone 1 2 >> end >> >> bond s 1 2 >> s 1 3 >> s 1 23 >> s 1 24 >> end >> END >> >> And the error: >> NATURAL BOND ORBITAL ANALYSIS: >> >> Error in input of bond orbitals: >> Keyword for orbital type is not LONE, BOND, or 3CBOND (read `1 ') >> >> I don't want to specify all the lone pairs, bonds and 3cbonds >> because my molecule is rather big. I've tried to put only the 3cbond >> keyword and I get only 2 units (instead of 10 that I get without >> it) but I need only 1 unit, so I'm putting these bonds. >> Can someone help me please? >> Thanks!> >> >> > > ---------------------------------------------------------------- > This message was sent using IMP, the Internet Messaging Program.http://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. From owner-chemistry@ccl.net Mon Aug 27 09:18:01 2007 From: "Wolf Ihlenfeldt wdi * xemistry.com" To: CCL Subject: CCL: Looking for freeware to compute Tanimoto coefficient Message-Id: <-35033-070826180305-26515-7dxA4puO+Ixm15Y2TXMHTQ!=!server.ccl.net> X-Original-From: "Wolf Ihlenfeldt" Content-Type: multipart/alternative; boundary="----=_Part_38207_24778479.1188161965282" Date: Sun, 26 Aug 2007 22:59:25 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf Ihlenfeldt" [wdi!^!xemistry.com] ------=_Part_38207_24778479.1188161965282 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline Or much simpler by replacing the explicit mathematics by prop compare E_SCREEN $scr1 $scr2 tanimoto On 8/23/07, Igor Filippov Contr igorf(0)helix.nih.gov < owner-chemistry+*+ccl.net> wrote: > > > Sent to CCL by: "Igor Filippov [Contr]" [igorf ~~ helix.nih.gov] > A simple CACTVS script can do this for you too: > > ---------------------------- > > set smiles1 [lindex $argv 0] > set smiles2 [lindex $argv 1] > #prop setparam E_SCREEN extended 2 # to select extended fingerprint > > if {![catch {ens create $smiles1} eh1]} { > if {![catch {ens create $smiles2} eh2]} { > ens hadd $eh1 > ens hadd $eh2 > set scr1 [ens get $eh1 E_SCREEN] > set scr2 [ens get $eh2 E_SCREEN] > set l [string length $scr1] > set sum1 0 > set sum2 0 > set sum_both 0 > for {set i 0} {$i < $l} {incr i} { > set b1 [string index $scr1 $i] > set b2 [string index $scr2 $i] > set sum1 [expr {$sum1+$b1}] > set sum2 [expr {$sum2+$b2}] > set bb [expr {$b1 & $b2}] > set sum_both [expr {$sum_both+$bb}] > } > set tanimoto [expr {1.*$sum_both/($sum1+$sum2-$sum_both)}] > puts $tanimoto > } > } > exit > --------------------------------------- > > Igor > > > On Thu, 2007-08-23 at 13:07 +0400, chupvl chupvl_-_gmail.com wrote: > > Sent to CCL by: chupvl [chupvl=-=gmail.com] > > I think this feature is implemented mostly on chemical cartridges and > > chemical expert systems. > > But this cheminf feature is very simple by it's nature - maybe you have > > to write some kind of script using CDK (or any other descriptors package > > and) and simple math equitations. > > > > I think the Screening Assistant can do this work for you > > http://www.univ-orleans.fr/icoa/screeningassistant/index.html > > > > Vladimir Chupakhin > > PhD, Dpt. of Chemistry, MSU > > Moscow , Russia > > > > Szabolcs Csepregi scsepregi]~[chemaxon.com wrote: > > > > > > Sent to CCL by: Szabolcs Csepregi [scsepregi^-^chemaxon.com] > > > Hi Manali, > > > > > > You can perform this with the compr utility from the JChem Screen > > > package: > > > http://www.chemaxon.com/jchem/doc/user/Compr.html > > > > > > Alternatively, overlap analysis is available in Instant JChem with > > > similarity option. This will identify the most similar pairs in the > > > two tables depending on your options: > > > http://www.chemaxon.com/anim/ijc/Overlap_analysis.html > > > > > > All ChemAxon products are free under the academic license, and Instant > > > JChem local database mode is free for everyone. > > > > > > I hope this helps. > > > Szabolcs > > > > > > Szabolcs Csepregi, PhD > > > Director of Search Technologies, ChemAxon Ltd. > > > http://www.chemaxon.com > > > Skype: szabolcs.csepregi > > > Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 > > > > > > Manali Joshi manali_+_adrik.bchs.uh.edu wrote: > > >> Sent to CCL by: "Manali Joshi" [manali- -adrik.bchs.uh.edu] > > >> Hello, > > >> > > >> I am looking for freeware to compute the Tanimoto coefficients > > >> between small molecules. > > >> Specifically i would like to compare a few molecules against a small > > >> database. > > >> Thanks in advance. > > >> > > >> -Manalihttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > > > http://server.ccl.net/chemistry/announcements/conferences/> > > > > ------=_Part_38207_24778479.1188161965282 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline
 
Or much simpler by replacing the explicit mathematics by
 
prop compare E_SCREEN $scr1 $scr2 tanimoto
 


 
On 8/23/07, Igor Filippov Contr igorf(0)helix.nih.gov <owner-chemistry+*+ccl.net> wrote:

Sent to CCL by: "Igor Filippov [Contr]" [igorf ~~ helix.nih.gov ]
A simple CACTVS script can do this for you too:

----------------------------

set smiles1 [lindex $argv 0]
set smiles2 [lindex $argv 1]
#prop setparam E_SCREEN extended 2 # to select extended fingerprint

if {![catch {ens create $smiles1} eh1]} {
       if {![catch {ens create $smiles2} eh2]} {
               ens hadd $eh1
               ens hadd $eh2
               set scr1 [ens get $eh1 E_SCREEN]
               set scr2 [ens get $eh2 E_SCREEN]
               set l [string length $scr1]
               set sum1 0
               set sum2 0
               set sum_both 0
               for {set i 0} {$i < $l} {incr i} {
                   set b1 [string index $scr1 $i]
                   set b2 [string index $scr2 $i]
                   set sum1 [expr {$sum1+$b1}]
                   set sum2 [expr {$sum2+$b2}]
                   set bb [expr {$b1 & $b2}]
                   set sum_both [expr {$sum_both+$bb}]
               }
            set tanimoto [expr {1.*$sum_both/($sum1+$sum2-$sum_both)}]
            puts $tanimoto
           }
   }
exit
---------------------------------------

Igor


On Thu, 2007-08-23 at 13:07 +0400, chupvl chupvl_-_gmail.com wrote:
> Sent to CCL by: chupvl [chupvl=-=gmail.com]
> I think this feature is implemented mostly on chemical cartridges and
> chemical expert systems.
> But this cheminf feature is very simple by it's nature - maybe you have
> to write some kind of script using CDK (or any other descriptors package
> and) and simple math equitations.
>
> I think the Screening Assistant can do this work for you
> http://www.univ-orleans.fr/icoa/screeningassistant/index.html
>
> Vladimir Chupakhin
> PhD, Dpt. of Chemistry, MSU
> Moscow , Russia
>
> Szabolcs Csepregi scsepregi]~[chemaxon.com wrote:
> >
> > Sent to CCL by: Szabolcs Csepregi [scsepregi^-^ chemaxon.com]
> > Hi Manali,
> >
> > You can perform this with the compr utility from the JChem Screen
> > package:
> > http://www.chemaxon.com/jchem/doc/user/Compr.html
> >
> > Alternatively, overlap analysis is available in Instant JChem with
> > similarity option. This will identify the most similar pairs in the
> > two tables depending on your options:
> > http://www.chemaxon.com/anim/ijc/Overlap_analysis.html
> >
> > All ChemAxon products are free under the academic license, and Instant
> > JChem local database mode is free for everyone.
> >
> > I hope this helps.
> > Szabolcs
> >
> > Szabolcs Csepregi, PhD
> > Director of Search Technologies, ChemAxon Ltd.
> > http://www.chemaxon.com
> > Skype: szabolcs.csepregi
> > Tel: +36 1 3878564   Cell: +36 20 4219863   Fax: +36 1 4532659
> >
> > Manali Joshi manali_+_adrik.bchs.uh.edu wrote:
> >> Sent to CCL by: "Manali  Joshi" [manali- -adrik.bchs.uh.edu]
> >> Hello,
> >>
> >> I am looking for freeware to compute the Tanimoto coefficients
> >> between small molecules.
> >> Specifically i would like to compare a few molecules against a small
> >> database.
> >> Thanks in advance.
> >>
> >> -Manalihttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences:
> > http://server.ccl.net/chemistry/announcements/conferences/


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------=_Part_38207_24778479.1188161965282-- From owner-chemistry@ccl.net Mon Aug 27 10:40:00 2007 From: "Wolf Ihlenfeldt wdi-,-xemistry.com" To: CCL Subject: CCL: fragment-substructure search Message-Id: <-35034-070827103608-16684-uvQzj3GqZ5FEXaaNlnanjA:server.ccl.net> X-Original-From: "Wolf Ihlenfeldt" Content-Type: multipart/alternative; boundary="----=_Part_45082_13740143.1188221526620" Date: Mon, 27 Aug 2007 15:32:06 +0200 MIME-Version: 1.0 Sent to CCL by: "Wolf Ihlenfeldt" [wdi(-)xemistry.com] ------=_Part_45082_13740143.1188221526620 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline Here is the CACTVS version: match ss -mode distinct c1ccccc1 c1ccc2ccccc2c1 Some fine points here: This mode will automatically filter out equivalent matches (the benzene fragment can match in 6 different orientations on the structure benzene ring). Other available modes allow you to filter out global equivalences (i.e. in unsubstituted napthalene the benzene rings are equivalent, so there will be only one hit), or to get the full match count (12, both rings with 6 orientations), and there more modes for additional fine-tuning. CACTVS supports SMARTS (with recursive SMARTS), ISIS query files, and SLN as query input. On 8/24/07, Szabolcs Csepregi scsepregi(~)chemaxon.com < owner-chemistry%ccl.net> wrote: > > Sent to CCL by: Szabolcs Csepregi [scsepregi*|*chemaxon.com] Hi Efrat, > > JChem can do that in many ways: > > 1. There is a JChem Oracle Cartridge operator jc_matchcount: > > http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_matchcount > > 2. The jcsearch command-line program can do this also using the "-t:c > --allHits" option: > > $ jcsearch -t:c --allHits -q c1ccccc1 c1ccc2ccccc2c1 > 2 > > See: http://www.chemaxon.com/jchem/doc/user/Jcsearch.html > > 3. There is a matchCount function in the Chemical Terms language for this. > This language can be used in many places at various ChemAxon products, for > example you can set up calculated columns in Instant JChem or JChem Base. > For more information, see: > > http://www.chemaxon.com/instantjchem/ijc_2_0/docs/user/help/htmlfiles/chemical_terms/adding_chem_terms_fields.html > http://www.chemaxon.com/chemterms.html > http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#matchcountdesc > > > 4. There are also a function in the programming interface: > MolSearch.getMatchCount() > See: > http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/MolSearch.html > > http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/Search.html#getMatchCount%28%29 > > > All of the above understands many file formats and can handle various > query features such as SMARTS, etc. > Probably the most straightforward to use is 3 (Instant JChem), which > happens to be free for local database usage. > > I hope this helps. > Szabolcs > > Szabolcs Csepregi, PhD > Director of Search Technologies, ChemAxon Ltd.http://www.chemaxon.com > Skype: szabolcs.csepregi > Tel: +36 1 3878564 Cell: +36 20 4219863 Fax: +36 1 4532659 > > > Efrat Noy enoy%a%epixpharma.com wrote: > > Sent to CCL by: "Efrat Noy" [enoy++epixpharma.com] > Hi All, > > I am looking for a tool capable of counting non-overlapping instances of substructure-fragments in a set of molecules, yet counting partially overlapping fragments. For example, counting two instances of a benzene fragment in a naphtalene molecule. > > Are you familiar with any tool able to do that? > > Thanks > > > > > enoy]_[epixpharma.comE-mail to subscribers: CHEMISTRY],[ccl.net or use:> > E-mail to administrators: CHEMISTRY-REQUEST],[ccl.net or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtTo > 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. E-mail to subscribers: > CHEMISTRY%ccl.net or use:E-mail to administrators: > CHEMISTRY-REQUEST%ccl.net or useBefore posting, check wait > time at: http://www.ccl.netConferences: > 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/------=_Part_45082_13740143.1188221526620 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: 7bit Content-Disposition: inline
 
Here is the CACTVS version:
 
match ss -mode distinct c1ccccc1 c1ccc2ccccc2c1
 
Some fine points here: This mode will automatically filter out equivalent matches
 (the benzene fragment can match in 6 different orientations on the structure benzene ring).
 
Other available modes allow you to filter out global equivalences
(i.e. in unsubstituted  napthalene the benzene rings are equivalent, so there will be only one hit), or to get the full match count
(12, both rings with 6 orientations), and there more modes for additional fine-tuning.
CACTVS supports SMARTS (with recursive SMARTS), ISIS query files, and SLN as query input.


 
On 8/24/07, Szabolcs Csepregi scsepregi(~)chemaxon.com <owner-chemistry%ccl.net> wrote:
Sent to CCL by: Szabolcs Csepregi [scsepregi*|* chemaxon.com]
Hi Efrat,

JChem can do that in many ways:

1. There is a JChem Oracle Cartridge operator jc_matchcount:
http://www.chemaxon.com/jchem/doc/guide/cartridge/cartapi.html#jc_matchcount

2.  The jcsearch command-line program can do this also using the "-t:c --allHits" option:

$ jcsearch -t:c --allHits -q c1ccccc1 c1ccc2ccccc2c1
2

See: http://www.chemaxon.com/jchem/doc/user/Jcsearch.html

3. There is a matchCount function in the Chemical Terms language for this. This language can be used in many places at various ChemAxon products, for example you can set up calculated columns in Instant JChem or JChem Base.
For more information, see:
http://www.chemaxon.com/instantjchem/ijc_2_0/docs/user/help/htmlfiles/chemical_terms/adding_chem_terms_fields.html
http://www.chemaxon.com/chemterms.html
http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#matchcountdesc


4. There are also a function in the programming interface: MolSearch.getMatchCount()
See:
http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/MolSearch.html
http://www.chemaxon.com/jchem/doc/api/chemaxon/sss/search/Search.html#getMatchCount%28%29

All of the above understands many file formats and can handle various query features such as SMARTS, etc.
Probably the most straightforward to use is 3 (Instant JChem), which happens to be free for local database usage.

I hope this helps.
Szabolcs 
Szabolcs Csepregi, PhD
Director of Search Technologies, ChemAxon Ltd.
http://www.chemaxon.com
Skype: szabolcs.csepregi
Tel: +36 1 3878564   Cell: +36 20 4219863   Fax: +36 1 4532659

Efrat Noy enoy%a%epixpharma.com wrote: 
Sent to CCL by: "Efrat  Noy" [enoy++epixpharma.com]
Hi All,

I am looking for a tool capable of counting non-overlapping instances of substructure-fragments in a set of molecules, yet counting partially overlapping fragments. For example, counting two instances of a benzene fragment in a naphtalene molecule. 

Are you familiar with any tool able to do that? 

Thanks




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------=_Part_45082_13740143.1188221526620-- From owner-chemistry@ccl.net Mon Aug 27 13:27:01 2007 From: "my-phuong pham phmphuong[a]yahoo.com" To: CCL Subject: CCL:G: run solvent in Gaussian Message-Id: <-35035-070827124509-22087-9D/I3oFj3niYCMV93Z1Luw**server.ccl.net> X-Original-From: "my-phuong pham" Date: Mon, 27 Aug 2007 12:45:04 -0400 Sent to CCL by: "my-phuong pham" [phmphuong.:.yahoo.com] > From: my-phuong pham phmphuong|a|yahoo.com I have the optimized TS strcutre in gas phase and I want to calculate SCF of it in solvent. Here are the input and output and I don't satisfy with the error notice in the output file: UA0: Hydrogen 40 is unbound. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. %chk=e1P_ts_sol.chk %mem=600mb %nprocl=1 %nprocs=2 p b3lyp/6-31g(d,p) SCF=Tight SCRF=(PCM,Solvent=Chloroform) Test nosym e1P_ts_sol 0 1 C 0.00402900 -0.20828000 -1.13297500 C 0.16651600 1.13160700 -1.76060400 H -0.79808000 -0.28572500 -0.41306000 H 0.10681000 -1.03922100 -1.81755800 H 1.01177700 1.16692400 -2.46789800 O -1.07075800 0.93710500 -2.35854000 C 0.19555600 2.39892900 -0.90625300 H -0.02649100 3.22903100 -1.59263800 H -0.60180800 2.37803300 -0.15101600 O 1.46833400 2.60335800 -0.28350800 C 1.71515100 3.96299100 0.02591700 H 2.70366700 4.02078600 0.48939500 H 1.70956700 4.58783100 -0.87896500 H 0.96903500 4.36871100 0.72650300 H -2.17804400 1.15158200 -1.30274500 C -3.67865300 0.24180200 -0.39140700 C -3.77166900 -0.76995500 -1.36531600 C -4.54532500 0.20561300 0.71490900 C -4.71454300 -1.78730800 -1.22384200 H -3.10089200 -0.73894900 -2.21834600 C -5.48188900 -0.81803400 0.84160000 H -4.47361200 0.99786500 1.45457900 C -5.57468100 -1.82410300 -0.12380500 H -4.77679100 -2.56025400 -1.98595000 H -6.14811600 -0.82743900 1.70087800 H -6.30754900 -2.61891400 -0.02292300 C 2.53621100 -1.11697100 -0.32928600 C 2.92297700 -2.45415300 -0.48617400 C 3.45309800 -0.08633000 -0.57529400 C 4.22692600 -2.75941500 -0.87588900 H 2.19265000 -3.23546300 -0.29906800 C 4.75486000 -0.40526900 -0.96474300 H 3.12497100 0.94394600 -0.47975300 C 5.14829200 -1.73710500 -1.11367600 H 4.52265300 -3.79792500 -0.99556300 H 5.46488400 0.39405600 -1.15875200 H 6.16235100 -1.97653700 -1.41917200 O -2.77747200 1.24399700 -0.46969000 O 1.24882200 -0.84546600 0.07207800 H 1.07245500 -0.44149800 1.19919500 N 0.79763000 -0.12051100 2.40464900 C -0.66892900 0.09025900 2.49235900 H -0.97672100 0.87863300 1.80359900 H -1.18299100 -0.83067200 2.21051500 H -0.95617500 0.36424100 3.51415500 C 1.54494900 1.11784700 2.72429700 H 2.61503700 0.90227900 2.69708000 H 1.32565800 1.86357500 1.95902900 H 1.27424900 1.48946700 3.71954400 C 1.22383100 -1.25367900 3.25537700 H 0.68342000 -2.15176400 2.95025400 H 2.29384100 -1.42232500 3.11940700 H 1.01917900 -1.04931600 4.31284100 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx The output: Entering Gaussian System, Link 0=g03 Input=e1P_ts_sol.com Output=e1P_ts_sol.log Initial command: /uufs/arches/sys/g03/g03/l1.exe /scratch/parallel/u0400086/180337.mmrm.privatearch.arches/Gau-2808.inp -scrdir=/scratch/parallel/u0400086/180337.mmrm.privatearch.arches/ Entering Link 1 = /uufs/arches/sys/g03/g03/l1.exe PID= 2810. Copyright (c) 1988,1990,1992,1993,1995,1998,2003,2004, Gaussian, Inc. All Rights Reserved. This is the Gaussian(R) 03 program. It is based on the the Gaussian(R) 98 system (copyright 1998, Gaussian, Inc.), the Gaussian(R) 94 system (copyright 1995, Gaussian, Inc.), the Gaussian 92(TM) system (copyright 1992, Gaussian, Inc.), the Gaussian 90(TM) system (copyright 1990, Gaussian, Inc.), the Gaussian 88(TM) system (copyright 1988, Gaussian, Inc.), the Gaussian 86(TM) system (copyright 1986, Carnegie Mellon University), and the Gaussian 82(TM) system (copyright 1983, Carnegie Mellon University). Gaussian is a federally registered trademark of Gaussian, Inc. This software contains proprietary and confidential information, including trade secrets, belonging to Gaussian, Inc. This software is provided under written license and may be used, copied, transmitted, or stored only in accord with that written license. The following legend is applicable only to US Government contracts under FAR: RESTRICTED RIGHTS LEGEND Use, reproduction and disclosure by the US Government is subject to restrictions as set forth in subparagraphs (a) and (c) of the Commercial Computer Software - Restricted Rights clause in FAR 52.227-19. Gaussian, Inc. 340 Quinnipiac St., Bldg. 40, Wallingford CT 06492 --------------------------------------------------------------- Warning -- This program may not be used in any manner that competes with the business of Gaussian, Inc. or will provide assistance to any competitor of Gaussian, Inc. The licensee of this program is prohibited from giving any competitor of Gaussian, Inc. access to this program. By using this program, the user acknowledges that Gaussian, Inc. is engaged in the business of creating and licensing software in the field of computational chemistry and represents and warrants to the licensee that it is not a competitor of Gaussian, Inc. and that it will not use this program in any manner prohibited above. --------------------------------------------------------------- Cite this work as: Gaussian 03, Revision D.01, M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Wallingford CT, 2004. ****************************************** Gaussian 03: AM64L-G03RevD.01 13-Oct-2005 22-Aug-2007 ****************************************** %chk=e1P_ts_sol.chk %mem=600mb %nprocl=1 Will use up to 1 processors via Linda. %nprocs=2 Will use up to 2 processors via shared memory. ---------------------------------------------------------------------- p b3lyp/6-31g(d,p) SCF=Tight SCRF=(PCM,Solvent=Chloroform) Test nosym ---------------------------------------------------------------------- 1/38=1/1; 2/15=1,17=6,18=5,40=1/2; 3/5=1,6=6,7=101,11=2,16=1,25=1,30=1,70=2201,72=7,74=-5/1,2,3; 4//1; 5/5=2,32=2,38=5,53=7/2; 6/7=2,8=2,9=2,10=2,28=1/1; 99/5=1,9=1/99; Leave Link 1 at Wed Aug 22 18:42:15 2007, MaxMem= 78643200 cpu: 14.5 (Enter /uufs/arches/sys/g03/g03/l101.exe) ---------- e1P_ts_sol ---------- Symbolic Z-matrix: Charge = 0 Multiplicity = 1 C 0.00403 -0.20828 -1.13298 C 0.16652 1.13161 -1.7606 H -0.79808 -0.28573 -0.41306 H 0.10681 -1.03922 -1.81756 H 1.01178 1.16692 -2.4679 O -1.07076 0.93711 -2.35854 C 0.19556 2.39893 -0.90625 H -0.02649 3.22903 -1.59264 H -0.60181 2.37803 -0.15102 O 1.46833 2.60336 -0.28351 C 1.71515 3.96299 0.02592 H 2.70367 4.02079 0.4894 H 1.70957 4.58783 -0.87897 H 0.96904 4.36871 0.7265 H -2.17804 1.15158 -1.30275 C -3.67865 0.2418 -0.39141 C -3.77167 -0.76996 -1.36532 C -4.54533 0.20561 0.71491 C -4.71454 -1.78731 -1.22384 H -3.10089 -0.73895 -2.21835 C -5.48189 -0.81803 0.8416 H -4.47361 0.99787 1.45458 C -5.57468 -1.8241 -0.12381 H -4.77679 -2.56025 -1.98595 H -6.14812 -0.82744 1.70088 H -6.30755 -2.61891 -0.02292 C 2.53621 -1.11697 -0.32929 C 2.92298 -2.45415 -0.48617 C 3.4531 -0.08633 -0.57529 C 4.22693 -2.75942 -0.87589 H 2.19265 -3.23546 -0.29907 C 4.75486 -0.40527 -0.96474 H 3.12497 0.94395 -0.47975 C 5.14829 -1.73711 -1.11368 H 4.52265 -3.79793 -0.99556 H 5.46488 0.39406 -1.15875 H 6.16235 -1.97654 -1.41917 O -2.77747 1.244 -0.46969 O 1.24882 -0.84547 0.07208 H 1.07245 -0.4415 1.1992 N 0.79763 -0.12051 2.40465 C -0.66893 0.09026 2.49236 H -0.97672 0.87863 1.8036 H -1.18299 -0.83067 2.21052 H -0.95618 0.36424 3.51416 C 1.54495 1.11785 2.7243 H 2.61504 0.90228 2.69708 H 1.32566 1.86358 1.95903 H 1.27425 1.48947 3.71954 C 1.22383 -1.25368 3.25538 H 0.68342 -2.15176 2.95025 H 2.29384 -1.42233 3.11941 H 1.01918 -1.04932 4.31284 Isotopes and Nuclear Properties: (Nuclear quadrupole moments (NQMom) in fm**2, nuclear magnetic moments (NMagM) in nuclear magnetons) Atom 1 2 3 4 5 6 7 8 9 10 IAtWgt= 12 12 1 1 1 16 12 1 1 16 AtmWgt= 12.0000000 12.0000000 1.0078250 1.0078250 1.0078250 15.9949146 12.0000000 1.0078250 1.0078250 15.9949146 NucSpn= 0 0 1 1 1 0 0 1 1 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 0.0000000 2.7928460 2.7928460 2.7928460 0.0000000 0.0000000 2.7928460 2.7928460 0.0000000 Atom 11 12 13 14 15 16 17 18 19 20 IAtWgt= 12 1 1 1 1 12 12 12 12 1 AtmWgt= 12.0000000 1.0078250 1.0078250 1.0078250 1.0078250 12.0000000 12.0000000 12.0000000 12.0000000 1.0078250 NucSpn= 0 1 1 1 1 0 0 0 0 1 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 2.7928460 2.7928460 2.7928460 2.7928460 0.0000000 0.0000000 0.0000000 0.0000000 2.7928460 Atom 21 22 23 24 25 26 27 28 29 30 IAtWgt= 12 1 12 1 1 1 12 12 12 12 AtmWgt= 12.0000000 1.0078250 12.0000000 1.0078250 1.0078250 1.0078250 12.0000000 12.0000000 12.0000000 12.0000000 NucSpn= 0 1 0 1 1 1 0 0 0 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.0000000 2.7928460 0.0000000 2.7928460 2.7928460 2.7928460 0.0000000 0.0000000 0.0000000 0.0000000 Atom 31 32 33 34 35 36 37 38 39 40 IAtWgt= 1 12 1 12 1 1 1 16 16 1 AtmWgt= 1.0078250 12.0000000 1.0078250 12.0000000 1.0078250 1.0078250 1.0078250 15.9949146 15.9949146 1.0078250 NucSpn= 1 0 1 0 1 1 1 0 0 1 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 2.7928460 0.0000000 2.7928460 0.0000000 2.7928460 2.7928460 2.7928460 0.0000000 0.0000000 2.7928460 Atom 41 42 43 44 45 46 47 48 49 50 IAtWgt= 14 12 1 1 1 12 1 1 1 12 AtmWgt= 14.0030740 12.0000000 1.0078250 1.0078250 1.0078250 12.0000000 1.0078250 1.0078250 1.0078250 12.0000000 NucSpn= 2 0 1 1 1 0 1 1 1 0 AtZEff= 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NQMom= 2.0440000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 NMagM= 0.4037610 0.0000000 2.7928460 2.7928460 2.7928460 0.0000000 2.7928460 2.7928460 2.7928460 0.0000000 Atom 51 52 53 IAtWgt= 1 1 1 AtmWgt= 1.0078250 1.0078250 1.0078250 NucSpn= 1 1 1 AtZEff= 0.0000000 0.0000000 0.0000000 NQMom= 0.0000000 0.0000000 0.0000000 NMagM= 2.7928460 2.7928460 2.7928460 Leave Link 101 at Wed Aug 22 18:42:24 2007, MaxMem= 78643200 cpu: 3.8 (Enter /uufs/arches/sys/g03/g03/l202.exe) Symmetry turned off by external request. Stoichiometry C19H29NO4 Framework group C1[X(C19H29NO4)] Deg. of freedom 153 Full point group C1 Z-Matrix orientation: --------------------------------------------------------------------- Center Atomic Atomic Coordinates (Angstroms) Number Number Type X Y Z --------------------------------------------------------------------- 1 6 0 0.004029 -0.208280 -1.132975 2 6 0 0.166516 1.131607 -1.760604 3 1 0 -0.798080 -0.285725 -0.413060 4 1 0 0.106810 -1.039221 -1.817558 5 1 0 1.011777 1.166924 -2.467898 6 8 0 -1.070758 0.937105 -2.358540 7 6 0 0.195556 2.398929 -0.906253 8 1 0 -0.026491 3.229031 -1.592638 9 1 0 -0.601808 2.378033 -0.151016 10 8 0 1.468334 2.603358 -0.283508 11 6 0 1.715151 3.962991 0.025917 12 1 0 2.703667 4.020786 0.489395 13 1 0 1.709567 4.587831 -0.878965 14 1 0 0.969035 4.368711 0.726503 15 1 0 -2.178044 1.151582 -1.302745 16 6 0 -3.678653 0.241802 -0.391407 17 6 0 -3.771669 -0.769955 -1.365316 18 6 0 -4.545325 0.205613 0.714909 19 6 0 -4.714543 -1.787308 -1.223842 20 1 0 -3.100892 -0.738949 -2.218346 21 6 0 -5.481889 -0.818034 0.841600 22 1 0 -4.473612 0.997865 1.454579 23 6 0 -5.574681 -1.824103 -0.123805 24 1 0 -4.776791 -2.560254 -1.985950 25 1 0 -6.148116 -0.827439 1.700878 26 1 0 -6.307549 -2.618914 -0.022923 27 6 0 2.536211 -1.116971 -0.329286 28 6 0 2.922977 -2.454153 -0.486174 29 6 0 3.453098 -0.086330 -0.575294 30 6 0 4.226926 -2.759415 -0.875889 31 1 0 2.192650 -3.235463 -0.299068 32 6 0 4.754860 -0.405269 -0.964743 33 1 0 3.124971 0.943946 -0.479753 34 6 0 5.148292 -1.737105 -1.113676 35 1 0 4.522653 -3.797925 -0.995563 36 1 0 5.464884 0.394056 -1.158752 37 1 0 6.162351 -1.976537 -1.419172 38 8 0 -2.777472 1.243997 -0.469690 39 8 0 1.248822 -0.845466 0.072078 40 1 0 1.072455 -0.441498 1.199195 41 7 0 0.797630 -0.120511 2.404649 42 6 0 -0.668929 0.090259 2.492359 43 1 0 -0.976721 0.878633 1.803599 44 1 0 -1.182991 -0.830672 2.210515 45 1 0 -0.956175 0.364241 3.514155 46 6 0 1.544949 1.117847 2.724297 47 1 0 2.615037 0.902279 2.697080 48 1 0 1.325658 1.863575 1.959029 49 1 0 1.274249 1.489467 3.719544 50 6 0 1.223831 -1.253679 3.255377 51 1 0 0.683420 -2.151764 2.950254 52 1 0 2.293841 -1.422325 3.119407 53 1 0 1.019179 -1.049316 4.312841 --------------------------------------------------------------------- Rotational constants (GHZ): 0.3039285 0.1255011 0.1204208 Leave Link 202 at Wed Aug 22 18:42:36 2007, MaxMem= 78643200 cpu: 6.0 (Enter /uufs/arches/sys/g03/g03/l301.exe) Standard basis: 6-31G(d,p) (6D, 7F) Integral buffers will be 131072 words long. Raffenetti 2 integral format. Two-electron integral symmetry is turned off. 505 basis functions, 875 primitive gaussians, 505 cartesian basis functions 91 alpha electrons 91 beta electrons nuclear repulsion energy 2155.5365968551 Hartrees. IExCor= 402 DFT=T Ex=B+HF Corr=LYP ExCW=0 ScaHFX= 0.200000 ScaDFX= 0.800000 0.720000 1.000000 0.810000 IRadAn= 0 IRanWt= -1 IRanGd= 0 ICorTp=0 NAtoms= 53 NActive= 53 NUniq= 53 SFac= 7.50D-01 NAtFMM= 80 NAOKFM=F Big=F ------------------------------------------------------------------------------ United Atom Topological Model (UA0 parameters set). UA0: Hydrogen 40 is unbound. Keep it explicit at all point on the UA0: potential energy surface to get meaningful results. Error termination via Lnk1e in /uufs/arches/sys/g03/g03/l301.exe at Wed Aug 22 18:42:57 2007. Job cpu time: 0 days 0 hours 0 minutes 18.0 seconds. File lengths (MBytes): RWF= 144 Int= 0 D2E= 0 Chk= 8 Scr= 8 From owner-chemistry@ccl.net Mon Aug 27 14:02:01 2007 From: "Oliver Welz oliver.welz**chemie.uni-karlsruhe.de" To: CCL Subject: CCL:G: Hessian in mass-weighted internal coordinates Message-Id: <-35036-070827113126-10845-1dsOW4BgeyDb/slBg8DKHA]![server.ccl.net> X-Original-From: "Oliver Welz" Date: Mon, 27 Aug 2007 11:31:22 -0400 Sent to CCL by: "Oliver Welz" [oliver.welz .. chemie.uni-karlsruhe.de] Hello, is there any possibility in GAUSSIAN 03 to extract the hessian in mass-weighted internal coordinates? I only obtained the hessian in cartesian and internal coordinates (but not in mass-weighted!) by using the "p" command in the input file. Thank you in advance. Oliver Oliver Welz Institut fr Physikalische Chemie Universitt Karlsruhe (TH) Fritz Haber Weg 4 76131 Karlsruhe oliver.welz=-=chemie.uni-karlsruhe.de From owner-chemistry@ccl.net Mon Aug 27 20:01:00 2007 From: "Jimmy Lawrence jlawrence###slb.com" To: CCL Subject: CCL:G: MFI, zeolite structure with Gaussian03 Message-Id: <-35037-070827125324-23533-hFgECIwWDYZP0MXN2RoY9w * server.ccl.net> X-Original-From: Jimmy Lawrence Content-transfer-encoding: 7BIT Content-type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 27 Aug 2007 12:04:43 -0400 MIME-version: 1.0 Sent to CCL by: Jimmy Lawrence [jlawrence:-:slb.com] Vincent, and other CCLers, Thanks for the info. However I cannot open the cif file. GaussView mentioned an error as below: CConnectionCIF::ReadMolecule() Failure reading crystal information from CIF file. File contains incomplete or unrecognized atomic symbol data. Line Number 63 Is it correct to change all the "T" symbol to "Si" ? And what will be the default steps to load gas molecules in to this framework ? Great thanks, Jimmy Lawrence Failure Vincent Xianlong Wang xloongw+/-yahoo.com wrote: > Sent to CCL by: Vincent Xianlong Wang [xloongw||yahoo.com] > Hi Jimmy, > > There is a good source for zeolite structure called > Database of Zeolite Structures. Here is the link, > http://www.iza-structure.org/databases/. > You can download the CIF file of the zeolite from the > website and open it in GaussView. > > Best regards, > Vincent > > --- "Jimmy Lawrence jlawrence%x%slb.com" > wrote: > >> Sent to CCL by: Jimmy Lawrence [jlawrence{:}slb.com] >> Hi CCL members, >> >> I am a beginner in calculating this type of >> system. >> Can somebody point a tutorial or share some >> experience by simple >> instruction on how to build the structure of MFI (or >> other zeolite) with >> PBC in Gaussian03 (via GaussView) and how to dock >> the molecule to >> evaluate (e.g. CO2) ? >> >> Thank you, >> >> Jimmy >> >> >> >> -= 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.> >> E-mail to administrators: CHEMISTRY-REQUEST(!)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/> >> >> >> > > > > > ____________________________________________________________________________________ > Be a better Globetrotter. Get better travel answers from someone who knows. Yahoo! Answers - Check it out. > http://answers.yahoo.com/dir/?link=list&sid=396545469> > > >