From owner-chemistry@ccl.net Wed Dec 5 00:02:00 2007 From: "Dipankar Roy dipankarroy],[iitb.ac.in" To: CCL Subject: CCL:G: GAUSSIAN MISTAKE Message-Id: <-35766-071204231430-23711-3s7dA6s3iGvgVW68U3wihw\a/server.ccl.net> X-Original-From: "Dipankar Roy" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Wed, 5 Dec 2007 08:44:15 +0530 (IST) MIME-Version: 1.0 Sent to CCL by: "Dipankar Roy" [dipankarroy . iitb.ac.in] Hi, Gaussian is not that efficient for AIM analysis. You can do an optimization and then generate a wave function file to use it with the codes like AIM200 (www.aim2000.de) or AIMPAC. regards, dipankar > > Sent to CCL by: "Diego Armando Gomez" [darkego21=-=yahoo.com] > Dear subscribers > > I'm from Bogota- Colombia, and my English is not good. Please Excuse me. > > I got the next mistake with GAUSSIAN03: > > The Hopf-Poincare condition cannot be satisfied. > Apparently some critical points are missing. Abort! > Error termination via Lnk1e in /opt/gaussian/g03/l609.exe at Tue Dec 4 > 13:30:33 2007. > > I am doing some calculations of the molecular interaction between VO2+ y > the USY zeolite. the commands line or route section was: > > # opt=modredundant rb3lyp/lanl2dz aim=all > > thanks a lot for any answer. > > Diego Gomez. > Bogota/Colombia> > > *********************************************** Dipankar Roy Graduate Student of Prof. R. B. Sunoj Computational Chemistry Laboratory Dept. of Chemistry Indian Institute of Technology, Bombay India - 400076 Phone: +91-22-2576-4130(lab) URL: http://www.geocities.com/dipankar_roy79/dipankar.html *********************************************** A SCIENTIST IS SOMEONE WHOSE CURIOSITY SURVIVES EDUCATION'S ASSAULTS ON IT. - SIR HERMANN BONDI From owner-chemistry@ccl.net Wed Dec 5 03:04:00 2007 From: "Stan van Gisbergen vangisbergen*o*scm.com" To: CCL Subject: CCL: For file conversion in ADF-reg Message-Id: <-35767-071204104536-18267-fIhzHoBEvQNEt6LVHVmyCg%%server.ccl.net> X-Original-From: Stan van Gisbergen Content-Type: multipart/alternative; boundary=Apple-Mail-262--567406997 Date: Tue, 4 Dec 2007 16:45:24 +0100 Mime-Version: 1.0 (Apple Message framework v752.3) Sent to CCL by: Stan van Gisbergen [vangisbergen a scm.com] --Apple-Mail-262--567406997 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Dear Senthilnathan, Please send future support requests for ADF to SCM directly, or use our online ADF forum. If one is using the ADF-GUI (ADF graphical user interface) there is a simple step-by-step tutorial on how to make fragments for fragment analysis: http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_tutorial/ page123.html If you're making an ADF input file yourself, several examples explain how one can do fragment analysis, e.g.: http://www.scm.com/Doc/ Doc2007.01/ADF/Examples/page88.html If you are using different .run files, use full path names to the fragment files. Typically one will rename a fragment TAPE21 to a fragment.t21, like for example, CO.t21. This one can use as fragment in a further calculation: DEFINE xyzC=2.0053211 xyzOx=3.2501913 END atoms 1. Ni 0 0 0 2. C xyzC xyzC xyzC f=CO/1 3. C -xyzC -xyzC xyzC f=CO/2 4. C xyzC -xyzC -xyzC f=CO/3 5. C -xyzC xyzC -xyzC f=CO/4 6. O xyzOx xyzOx xyzOx f=CO/1 7. O -xyzOx -xyzOx xyzOx f=CO/2 8. O xyzOx -xyzOx -xyzOx f=CO/3 9. O -xyzOx xyzOx -xyzOx f=CO/4 end fragments CO t21.CO Ni t21.Ni end Best regards, Stan van Gisbergen On Dec 4, 2007, at 2:14 PM, senthil nathan zenthil03^yahoo.co.in wrote: > > Sent to CCL by: "senthil nathan" [zenthil03[-]yahoo.co.in] > Dear CCLrs, > In connection with my privious question, I want to do > fragment analysis for particular system. My total chemical system > is neutral, but its fragment is charged species. I have done a > calculation for both the fragment files separatly and I have two > TAPE21 file for my fragments. For total fragment analysis I want to > read some basic results form TAPE21 fragment file. Now I am using > ADF trial windows version, in this version TAPE21 file will be a > binary result file. I want to do this fragment TAPE21 file as input > file for total fragment analysis. I unable to convert this binary > file as a ADF input file. Any one of you tell me a better solution > for my problem. > > thanking you inadvance > best wishes from > Senthilnathan > > > > -= 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)> > Dr. S.J.A. van Gisbergen Scientific Computing & Modelling NV Theoretical Chemistry, Vrije Universiteit De Boelelaan 1083 1081 HV Amsterdam The Netherlands vangisbergen-x-scm.com http://www.scm.com T: +31-20-5987626 F: +31-20-5987629 --Apple-Mail-262--567406997 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1 Dear Senthilnathan,=A0

Please send future support = requests for ADF to SCM directly, or use our online ADF = forum.=A0

If one is using the ADF-GUI (ADF graphical user = interface) there is a simple step-by-step tutorial on=A0how to make = fragments for fragment analysis:=A0http://www.scm.com/Doc/Doc2007.01/ADFGUI/ADFGUI_tutorial/page123.html=

If you're = making an ADF input file yourself, several examples explain how one can = do=A0fragment analysis, e.g.:=A0http:/= /www.scm.com/Doc/Doc2007.01/ADF/Examples/page88.html

If you are using different .run files, use full path = names to the fragment files.=A0Typically one will rename a fragment = TAPE21 to a fragment.t21, like for example,=A0CO.t21.
This one can use as fragment in a further = calculation:

DEFINE
xyzOx=3D3.2501913
END

atoms
1. Ni =A0 0 =A0 =A0 =A0 0=A0 =A0 =A0 =A0 0=A0 2. C=A0 = =A0 xyzC=A0 =A0 xyzC =A0 =A0 xyzC =A0 =A0 f=3DCO/1
3. C =A0 -xyzC =A0 -xyzC =A0 =A0 xyzC =A0 =A0 = f=3DCO/2
4. C=A0 =A0 xyzC =A0 -xyzC=A0 =A0 = -xyzC =A0 =A0 f=3DCO/3
5. C =A0 -xyzC=A0 =A0 xyzC=A0= =A0 -xyzC =A0 =A0 f=3DCO/4
6. O=A0 =A0 = xyzOx =A0 xyzOx=A0 =A0 xyzOx =A0 =A0 f=3DCO/1
7. O =A0 -xyzOx=A0 -xyzOx=A0 =A0 xyzOx =A0 =A0 = f=3DCO/2
8. O=A0 =A0 xyzOx=A0 -xyzOx =A0 = -xyzOx =A0 =A0 f=3DCO/3
9. O =A0 = -xyzOx =A0 xyzOx =A0 -xyzOx =A0 =A0 f=3DCO/4
end

fragments
CO=A0 t21.CO
Ni=A0 = t21.Ni
end

Best = regards,
Stan van Gisbergen

On Dec 4, 2007, at = 2:14 PM, senthil nathan zenthil03^yahoo.co.in wrote:


Sent to = CCL by: "senthil=A0 nathan" = [zenthil03[-]yahoo.co.in]
Dear = CCLrs,
=A0 =A0 =A0 =A0 =A0 =A0 In = connection with my privious question, I want to do fragment analysis for = particular system. My total chemical system is neutral, but its fragment = is charged species. I have done a calculation for both the fragment = files separatly and I have two TAPE21 file for my fragments. For total = fragment analysis I want to read some basic results form TAPE21 fragment = file. Now I am using ADF trial windows version, in this version TAPE21 = file will be a binary result file. I want to do this fragment TAPE21 = file as input file for total fragment analysis. I unable to convert this = binary file as a ADF input file. Any one of you tell me a better = solution for my problem.

thanking you inadvance
best wishes from



-=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 -x- sign. You can also
look up = the X-Original-From: line in the mail header.

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E-mail to administrators: CHEMISTRY-REQUEST-x-ccl.net = or use

Subscribe/Unsubscribe:=A0

Before posting, check wait time = at: http://www.ccl.net

http:/= /server.ccl.net/chemistry/announcements/conferences/

Search = Messages: http://www.ccl.net/htdig=A0 (login: ccl, Password: = search)

If your mail bounces from CCL with 5.7.1 error, = check:






=
Dr. S.J.A. van Gisbergen
Scientific Computing & Modelling NV
Theoretical Chemistry, Vrije Universiteit
De Boelelaan 1083
1081 HV = Amsterdam
The Netherlands=A0=A0 =A0 =A0 =A0 = =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0

 =

= --Apple-Mail-262--567406997-- From owner-chemistry@ccl.net Wed Dec 5 05:37:00 2007 From: "may abdelghani may01dz{:}yahoo.fr" To: CCL Subject: CCL: RE : CCL: For file conversion in ADF-reg Message-Id: <-35768-071205034227-31221-ELjJR76Jei49Qp0WTL0ytw%a%server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-421104370-1196844132=:44149" Date: Wed, 5 Dec 2007 09:42:12 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz,yahoo.fr] --0-421104370-1196844132=:44149 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi; With the ADFGNU, you can do all this works…you can assign the charge to your fragment in very easy way… you can obtained an input, t21 and .out for each fragment, only follow the instruction present in ADFGUI_tutorial, on pages from 196 to 126. "senthil nathan zenthil03^yahoo.co.in" a écrit : Sent to CCL by: "senthil nathan" [zenthil03[-]yahoo.co.in] Dear CCLrs, In connection with my privious question, I want to do fragment analysis for particular system. My total chemical system is neutral, but its fragment is charged species. I have done a calculation for both the fragment files separatly and I have two TAPE21 file for my fragments. For total fragment analysis I want to read some basic results form TAPE21 fragment file. Now I am using ADF trial windows version, in this version TAPE21 file will be a binary result file. I want to do this fragment TAPE21 file as input file for total fragment analysis. I unable to convert this binary file as a ADF input file. Any one of you tell me a better solution for my problem. thanking you inadvance best wishes from Senthilnathanhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-421104370-1196844132=:44149 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi;
 
With the ADFGNU, you can do all this works…you can assign the charge to your fragment in very easy way… you can obtained an input, t21 and .out for each fragment, only follow the instruction present in ADFGUI_tutorial, on pages from 196 to 126.


"senthil nathan zenthil03^yahoo.co.in" <owner-chemistry:-:ccl.net> a écrit :

Sent to CCL by: "senthil nathan" [zenthil03[-]yahoo.co.in]
Dear CCLrs,
In connection with my privious question, I want to do fragment analysis for particular system. My total chemical system is neutral, but its fragment is charged species. I have done a calculation for both the fragment files separatly and I have two TAPE21 file for my fragments. For total fragment analysis I want to read some basic results form TAPE21 fragment file. Now I am using ADF trial windows version, in this version TAPE21 file will be a binary result file. I want to do this fragment TAPE21 file as input file for total fragment analysis. I unable to convert this binary file as a ADF input file. Any one of you tell me a better solution for my problem.

thanking you inadvance
best wishes from
Senthilnathan


http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/cgi-bin/ccl/send_ccl_message
http://www.ccl.net/chemistry/sub_unsub.shtml
http://www.ccl.net/spammers.txt



Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-421104370-1196844132=:44149-- From owner-chemistry@ccl.net Wed Dec 5 06:04:00 2007 From: "may abdelghani may01dz||yahoo.fr" To: CCL Subject: CCL: RE : CCL: structural isomerism and fluxional isomerism Message-Id: <-35769-071205054106-4187-vHYAmQBS5HBcIx1DWBfqWA*|*server.ccl.net> X-Original-From: may abdelghani Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-160917585-1196851250=:60114" Date: Wed, 5 Dec 2007 11:40:50 +0100 (CET) MIME-Version: 1.0 Sent to CCL by: may abdelghani [may01dz%a%yahoo.fr] --0-160917585-1196851250=:60114 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit dear CCLes The rapid rearrangement of the molecule's atoms, from one conformation to another is passed through a transition sates or not? Thank you very much sir, "akef afaneh akef_afnh=yahoo.com" a écrit : This is a very wide question. Fluxional molecules: molecules that exhibit rapid intramolecular rearrangements among their component atoms [E. L. Eliel, S. H. Wilen and L. N. Mander; Stereochemistry of Organic Compounds, JW 1994]. As in structural isomerism and tautomerism, fluxional compounds maintain the same number of component atoms. For example; keto-enol tautomerism (CH3COCH2CO2Et ¡ê CH3C(OH)=CHCO2Et) when warmed in the presence of base they become rapidly equilibrating and their NMR spectra may coalesce. Nevertheless, two molecular species still coexist, as can be readily verified by IR spectroscopy. Bullvalene represents another example of tautomerism called "valence tautomerism". This molecule exists 1,209,600 structures because there is a possibility of bond migration. Cyclohexane, the 1H-NMR spectrum at room temperature shows all protons are equivalent. The crystal structure of the complex [Co(abap)Cl2]Cl shows the presence of eight chemically inequivalent carbon atoms. However, the 13C NMR of this species in solution shows only 5 peaks.Why? The molecule is undergoing a fluxional process, which is rapid on the NMR timescale and results in the observation of the time-averaged signals from all the carbon atoms. This makes the two sets of propyl carbon atoms ¡°equivalent¡± and hence we only see 5 distinct signals. Finally, as the process gets faster still, A and B can no longer be distinguished and we only see one narrow peak at the average frequency of A and B. the peak appears narrow because, on NMR timescale, the molecule appears stationary and hence has infinite lifetime. Fluxional processes are temperature dependent. Their rate constant can be determined from the line-width of the peak and the activation parameters, Ea, ∆G¢Ô, ∆H¢Ô and ∆S¢Ô, at different temperature. You can see the following article: Quantum-mechanical calculations of the stabilities of fluxional isomers of C4H7+ in solution, Joseph Casanova, David R. Kent IV, William A. Goddard III, and John D. Roberts. I hope this information can help you. Best Regards Akef "may abdelghani may01dz#%#yahoo.fr" wrote: dear CCLers, First, what is the different between the structural isomerism and fluxional isomerism? How we can distinct between them? How we can expect, or study theoretically, the fluxional behaviour of some molecules (from the shape of the orbital and its interaction with each other, for exemple)? thanks --------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --------------------------------- Never miss a thing. Make Yahoo your homepage. --------------------------------- Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-160917585-1196851250=:60114 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
dear CCLes
 
The rapid rearrangement of the molecule's atoms, from one conformation to another is passed through a transition sates or not?
Thank you very much sir,


"akef afaneh akef_afnh=yahoo.com" <owner-chemistry^ccl.net> a écrit :
This is a very wide question. Fluxional molecules: molecules that exhibit rapid intramolecular rearrangements among their component atoms [E. L. Eliel, S. H. Wilen and L. N. Mander; Stereochemistry of Organic Compounds, JW 1994]. As in structural isomerism and tautomerism, fluxional compounds maintain the same number of component atoms. For example; keto-enol tautomerism (CH3COCH2CO2Et ¡ê CH3C(OH)=CHCO2Et) when warmed in the presence of base they become rapidly equilibrating and their NMR spectra may coalesce. Nevertheless, two molecular species still coexist, as can be readily verified by IR spectroscopy.
Bullvalene represents another example of tautomerism called "valence tautomerism". This molecule exists 1,209,600 structures because there is a possibility of bond migration.
Cyclohexane, the 1H-NMR spectrum at room temperature shows all protons are equivalent.
The crystal structure of the complex [Co(abap)Cl2]Cl shows the presence of eight chemically inequivalent carbon atoms. However, the 13C NMR of this species in solution shows only 5 peaks.Why?
The molecule is undergoing a fluxional process, which is rapid on the NMR timescale and results in the observation of the time-averaged signals from all the carbon atoms. This makes the two sets of propyl carbon atoms ¡°equivalent¡± and hence we only see 5 distinct signals.
Finally, as the process gets faster still, A and B can no longer be distinguished and we only see one narrow peak at the average frequency of A and B. the peak appears narrow because, on NMR timescale, the molecule appears stationary and hence has infinite lifetime. Fluxional processes are temperature dependent. Their rate constant can be determined from the line-width of the peak and the activation parameters, Ea, ∆G¢Ô, ∆H¢Ô and ∆S¢Ô, at different temperature.
You can see the following article: Quantum-mechanical calculations of the stabilities of fluxional isomers of C4H7+ in solution, Joseph Casanova, David R. Kent IV, William A. Goddard III, and John D. Roberts.
I hope this information can help you.
 
Best Regards
Akef
 
 
 
 


"may abdelghani may01dz#%#yahoo.fr" <owner-chemistry ~~ ccl.net> wrote:
dear CCLers,

First, what is the different between the structural isomerism and fluxional isomerism?
How we can distinct between them?
 How we can expect, or study theoretically, the fluxional behaviour of some molecules (from the shape of the orbital and its interaction with each other, for exemple)?

thanks

Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail

Never miss a thing. Make Yahoo your homepage.

Ne gardez plus qu'une seule adresse mail ! Copiez vos mails vers Yahoo! Mail --0-160917585-1196851250=:60114-- From owner-chemistry@ccl.net Wed Dec 5 08:32:00 2007 From: "Jian computationalboy**gmail.com" To: CCL Subject: CCL: Looking for a structure to name conversion software Message-Id: <-35770-071205082733-28297-kZSL/ekuTsPnuIaPx8pX7A . server.ccl.net> X-Original-From: Jian Content-Type: multipart/alternative; boundary="----=_Part_1259_29548916.1196859711328" Date: Wed, 5 Dec 2007 21:01:51 +0800 MIME-Version: 1.0 Sent to CCL by: Jian [computationalboy!=!gmail.com] ------=_Part_1259_29548916.1196859711328 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline ChemOffice may do that better, but it is commerical software. On Nov 16, 2007 6:39 PM, drmsaravanan=aim.com wrote: > > Hi All, > > Is there any tool to convert 1000 structures to name at a stretch? it > would be better if it is available freely. > > regards, > > M. Saravanan > ------------------------------ > *Check Out the new free AIM(R) Mail*-- Unlimited storage and industry-leading spam and email virus protection. > -- Arthur J. Wang Shenyang Pharmaceutical University P.O. Box 40 103 Wenhua Road, Shenhe District Shenyang,110016, P. R. China Tel : +86 24 23986419 Fax: +86 24 23995043 E-Mail: wjmed(a)126.com ; computationalboy(a)gmail.com ------=_Part_1259_29548916.1196859711328 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline ChemOffice may do that better, but it is commerical software.


On Nov 16, 2007 6:39 PM, drmsaravanan=aim.com <owner-chemistry(a)ccl.net > wrote:

Hi All,

Is there any tool  to convert 1000 structures to name at a stretch? it would be better if it is available freely.

regards,

M. Saravanan
Check Out the new free AIM(R) Mail -- Unlimited storage and industry-leading spam and email virus protection.



--
Arthur J. Wang
Shenyang Pharmaceutical University P.O. Box 40
103 Wenhua Road, Shenhe District
Shenyang,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail:  wjmed(a)126.com ;
     computationalboy(a)gmail.com ------=_Part_1259_29548916.1196859711328-- From owner-chemistry@ccl.net Wed Dec 5 09:07:00 2007 From: "Jian computationalboy * gmail.com" To: CCL Subject: CCL: Parallel implementation of AutoDock Message-Id: <-35771-071205084712-14071-u+DqcwOS+SoGaX3nI4Lilg\a/server.ccl.net> X-Original-From: Jian Content-Type: multipart/alternative; boundary="----=_Part_1185_16152658.1196858739524" Date: Wed, 5 Dec 2007 20:45:39 +0800 MIME-Version: 1.0 Sent to CCL by: Jian [computationalboy_+_gmail.com] ------=_Part_1185_16152658.1196858739524 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all: The official version of AutoDock cannot be used for parallelization. Khodade *et al.* developped the AutoDock program for parallel implementation, however, they didn't supply their codes in their paper. http://scripts.iucr.org/cgi-bin/paper?kk5006 Can anyone give me some instructions on how to parallel implementation of AutoDock? Thanks in advance! Yours Arthur ------=_Part_1185_16152658.1196858739524 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Content-Disposition: inline Dear all:

The official version of AutoDock cannot be used for parallelization.

Khodade et al. developped the AutoDock program for parallel implementation, however, they didn't supply their codes in their paper.

http://scripts.iucr.org/cgi-bin/paper?kk5006

Can anyone give me some instructions on how to parallel implementation of AutoDock?

Thanks in advance!

Yours Arthur
------=_Part_1185_16152658.1196858739524-- From owner-chemistry@ccl.net Wed Dec 5 10:15:01 2007 From: "DSprous|a|redpointbio.com" To: CCL Subject: CCL: Looking for a structure to name conversion software Message-Id: <-35772-071205101345-30931-6R59eHo5yTuc1cnzptpaTg*server.ccl.net> X-Original-From: Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C8374C.E2D1EA72" Date: Wed, 5 Dec 2007 09:41:14 -0500 MIME-Version: 1.0 Sent to CCL by: [DSprous-x-redpointbio.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C8374C.E2D1EA72 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable The options for converting names to structures are three companies/products: =20 1. ACD has a batch program. 2. Cambridgesoft has a batch program. 3. OpenEyes has a product LexiChem. =20 =20 I evaluated all three in 2006 and preferred Lexichem. =20 =20 I am unaware of any free software. =20 =20 -- Dennis=20 =20 Dennis G. Sprous, PhD Chemoinformatics/Computational Chemistry RedPointBio Inc. 7 Graphics Drive Ewing NJ 08628 609-637-9700 ________________________________ > From: owner-chemistry,+,ccl.net [mailto:owner-chemistry,+,ccl.net]=20 Sent: Wednesday, December 05, 2007 8:02 AM To: Dennis Sprous Subject: CCL: Looking for a structure to name conversion software =20 ChemOffice may do that better, but it is commerical software. On Nov 16, 2007 6:39 PM, drmsaravanan=3Daim.com = wrote: Hi All, Is there any tool to convert 1000 structures to name at a stretch? it would be better if it is available freely. regards, M. Saravanan ________________________________ Check Out the new free AIM(R) Mail -- Unlimited storage and industry-leading spam and email virus protection. --=20 Arthur J. Wang Shenyang Pharmaceutical University P.O. Box 40 103 Wenhua Road, Shenhe District Shenyang,110016, P. R. China=20 Tel : +86 24 23986419 Fax: +86 24 23995043=20 E-Mail: wjmed(~)126.com ;=20 computationalboy(~)gmail.com=20 ------_=_NextPart_001_01C8374C.E2D1EA72 Content-Type: text/html; charset="US-ASCII" Content-Transfer-Encoding: quoted-printable

The options for converting names to structures are three companies/products:

 

  1. ACD has a batch program.
  2. Cambridgesoft has a batch program.
  3. OpenEyes has a product LexiChem. 

 

I evaluated all three in 2006 and = preferred Lexichem. 

 

I am unaware of any free = software. 

 

-- Dennis =

 

Dennis G. Sprous, = PhD

Chemoinformatics/Computational = Chemistry

RedPointBio Inc.

7 Graphics Drive Ewing NJ 08628

609-637-9700

From: owner-chemistry,+,ccl.net [mailto:owner-chemistry,+,ccl.net]
Sent: Wednesday, December = 05, 2007 8:02 AM
To: Dennis Sprous
Subject: CCL: Looking for = a structure to name conversion software

 

ChemOffice may = do that better, but it is commerical software.

On Nov 16, 2007 6:39 PM, drmsaravanan=3Daim.com <owner-chemistry(~)ccl.net = > wrote:


Hi All,

Is there any tool  to convert 1000 structures to name at = a stretch? it would be better if it is available freely.

regards,

M. Saravanan

Check Out the new = free AIM(R) Mail -- Unlimited storage and industry-leading spam and = email virus protection.




--
Arthur J. Wang
Shenyang Pharmaceutical University P.O. Box = 40
103 Wenhua = Road, Shenhe District
Shenyang,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail:  wjmed(~)126.com ; =
     computationalboy(~)gmail.com=

------_=_NextPart_001_01C8374C.E2D1EA72-- From owner-chemistry@ccl.net Wed Dec 5 21:51:00 2007 From: "Antony Williams tony]![chemspider.com" To: CCL Subject: CCL: Looking for a structure to name conversion software Message-Id: <-35773-071205214645-7530-GdSaKIKxV14bemziIfyCTA{}server.ccl.net> X-Original-From: "Antony Williams" Content-class: urn:content-classes:message Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C837A8.F39F0960" Date: Wed, 5 Dec 2007 20:38:25 -0500 MIME-Version: 1.0 Sent to CCL by: "Antony Williams" [tony!A!chemspider.com] This is a multi-part message in MIME format. ------_=_NextPart_001_01C837A8.F39F0960 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable I am presently involved in writing a book chapter regarding Name to Structure conversion. Dennis, would you please contact me offline to discuss the objective criteria you used to compare the three products. Thanks=20 =20 Antony Williams, Host of ChemSpider (www.chemspider.com ) =20 Phone: (919) 341-8375 Mobile: (919) 201-1516 Fax: (919) 300 5321=20 Email: antony.williamsATchemspiderDOTcom =20 CONFIDENTIALITY NOTICE Unless expressly stated otherwise, this message is confidential and is intended for the addressee(s) only. If you are not an addressee, please inform the sender immediately or contact feedback!^!chemspider.com . ________________________________ > From: owner-chemistry!^!ccl.net [mailto:owner-chemistry!^!ccl.net]=20 Sent: Wednesday, December 05, 2007 9:41 AM To: Antony Williams Subject: CCL: Looking for a structure to name conversion software =20 The options for converting names to structures are three companies/products: =20 1. ACD has a batch program. 2. Cambridgesoft has a batch program. 3. OpenEyes has a product LexiChem. =20 =20 I evaluated all three in 2006 and preferred Lexichem. =20 =20 I am unaware of any free software. =20 =20 -- Dennis=20 =20 Dennis G. Sprous, PhD Chemoinformatics/Computational Chemistry RedPointBio Inc. 7 Graphics Drive Ewing NJ 08628 609-637-9700 ________________________________ > From: owner-chemistry.:.ccl.net [mailto:owner-chemistry.:.ccl.net]=20 Sent: Wednesday, December 05, 2007 8:02 AM To: Dennis Sprous Subject: CCL: Looking for a structure to name conversion software =20 ChemOffice may do that better, but it is commerical software. On Nov 16, 2007 6:39 PM, drmsaravanan=3Daim.com = wrote: Hi All, Is there any tool to convert 1000 structures to name at a stretch? it would be better if it is available freely. regards, M. Saravanan ________________________________ Check Out the new free AIM(R) Mail -- Unlimited storage and industry-leading spam and email virus protection. --=20 Arthur J. Wang Shenyang Pharmaceutical University P.O. Box 40 103 Wenhua Road, Shenhe District Shenyang,110016, P. R. China=20 Tel : +86 24 23986419 Fax: +86 24 23995043=20 E-Mail: wjmed(~)126.com ;=20 computationalboy(~)gmail.com=20 ------_=_NextPart_001_01C837A8.F39F0960 Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

I am presently involved in writing = a book chapter regarding Name to Structure conversion. Dennis, would you please contact me offline to discuss the objective criteria you used to compare = the three products. Thanks

 

Antony Williams,
Host of ChemSpider = (www.chemspider.com)

 

Phone: (919) 341-8375

Mobile: (919) 201-1516

Fax: (919) 300 5321 
Email: = antony.williamsATchemspiderDOTcom

 

CONFIDENTIALITY = NOTICE

Unless = expressly stated otherwise, this message is confidential and is intended for the = addressee(s) only.

If you are not = an addressee, please inform the sender immediately or contact = feedback!^!chemspider.com.

From: owner-chemistry!^!ccl.net [mailto:owner-chemistry!^!ccl.net]
Sent: Wednesday, December = 05, 2007 9:41 AM
To: Antony Williams
Subject: CCL: Looking for = a structure to name conversion software

 

The options for converting names to structures are three companies/products:

 

  1. ACD has a batch program.
  2. Cambridgesoft has a batch program.
  3. OpenEyes has a product LexiChem. 

 

I evaluated all three in 2006 and preferred Lexichem. 

 

I am unaware of any free = software. 

 

-- Dennis =

 

Dennis G. Sprous, = PhD

Chemoinformatics/Computational = Chemistry

RedPointBio Inc.

7 Graphics Drive Ewing NJ 08628

609-637-9700

From: owner-chemistry.:.ccl.net [mailto:owner-chemistry.:.ccl.net]
Sent: Wednesday, December = 05, 2007 8:02 AM
To: Dennis Sprous
Subject: CCL: Looking for = a structure to name conversion software

 

ChemOffice may = do that better, but it is commerical software.

On Nov 16, 2007 6:39 PM, drmsaravanan=3Daim.com <owner-chemistry(~)ccl.net = > wrote:


Hi All,

Is there any tool  to convert 1000 structures to name at = a stretch? it would be better if it is available freely.

regards,

M. Saravanan

Check Out the new = free AIM(R) Mail -- Unlimited storage and industry-leading spam and = email virus protection.




--
Arthur J. Wang
Shenyang Pharmaceutical University P.O. Box = 40
103 Wenhua = Road, Shenhe District
Shenyang,110016, P. R. China
Tel : +86 24 23986419
Fax: +86 24 23995043
E-Mail:  wjmed(~)126.com ; =
     computationalboy(~)gmail.com=

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