From owner-chemistry@ccl.net Tue Sep 8 02:35:01 2009 From: "Mingyue Zheng myzheng-x-gmail.com" To: CCL Subject: CCL: Chemical reactions and mol2 files Message-Id: <-40190-090908022735-19478-DkToLcB/I+VVYZFo9dqjsA~!~server.ccl.net> X-Original-From: Mingyue Zheng Content-Type: multipart/alternative; boundary=0015174be866a1450404730b0e3f Date: Tue, 8 Sep 2009 14:26:54 +0800 MIME-Version: 1.0 Sent to CCL by: Mingyue Zheng [myzheng.:.gmail.com] --0015174be866a1450404730b0e3f Content-Type: text/plain; charset=ISO-8859-1 You may try openbabel or pybel. 2009/9/6 Werner K werner.schroedinger^googlemail.com < owner-chemistry!^!ccl.net> > > Sent to CCL by: "Werner K" [werner.schroedinger,,googlemail.com] > Hi, > > I have a file in MOL2 format with around 10000 molecules. I want to perform > chemical reactions on them (for instance change all -OH to -COOH) and get > the results in MOL2 format with the corresponding new 3D coordinates for the > new functional groups, etc. > > What is the best software for this purpose? > > Thanks > > W> > > -- -------------------------------------------------------------------------------- Mingyue Zheng, Ph.D. Drug Discovery and Design Center (DDDC) Box 1201, Shanghai Institute of Materia Medica. 555 Rd. Zuchongzhi, Shanghai, China Tel: 86-021-50806600-1308 Email: myzheng!^!mail.shcnc.ac.cn --0015174be866a1450404730b0e3f Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable You may try openbabel or pybel.

2009/9/6 = Werner K werner.schroedinger^googlemail.c= om <own= er-chemistry!^!ccl.net>

Sent to CCL by: "Werner =A0K" [werner.schroedinger,,googlemail.com]
Hi,

I have a file in MOL2 format with around 10000 molecules. I want to perform= chemical reactions on them (for instance change all -OH to -COOH) and get = the results in MOL2 format with the corresponding new 3D coordinates for th= e new functional groups, etc.

What is the best software for this purpose?

Thanks

W



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--
-----------------------= ---------------------------------------------------------
Mingyue Zheng,= Ph.D.
Drug Discovery and Design Center (DDDC)
Box 1201, Shanghai Ins= titute of Materia Medica.
555 Rd. Zuchongzhi, Shanghai, China
Tel: =A0 =A0 =A086-021-50806600-1308=
Email: myzheng!^!mail.shcnc.a= c.cn
--0015174be866a1450404730b0e3f-- From owner-chemistry@ccl.net Tue Sep 8 04:14:00 2009 From: "andras.borosy%x%givaudan.com" To: CCL Subject: CCL: Compound retrosynthesis Message-Id: <-40191-090908041244-21901-cKobmiCCY5LrWMnaphiI3g^server.ccl.net> X-Original-From: andras.borosy-$-givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 0029EF1FC125762B_=" Date: Tue, 8 Sep 2009 09:38:01 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy(_)givaudan.com This is a multipart message in MIME format. --=_alternative 0029EF1FC125762B_= Content-Type: text/plain; charset="US-ASCII" Dear Bryan, It is not free, but pretty good: http://www.simbiosys.ca/archem/index.html Regards, Andras "Bryan Bishop kanzure%x%gmail.com" Sent by: owner-chemistry+andras.borosy==givaudan.com^^^ccl.net 08.09.2009 02:31 Please respond to "CCL Subscribers" To "Borosy, Andras " cc Subject CCL: Compound retrosynthesis Sent to CCL by: Bryan Bishop [kanzure[*]gmail.com] On Mon, Sep 7, 2009 at 4:10 PM, Werner K werner.schroedinger[*]gmail.com wrote: > given a certain compound, for instance caffeina, I am looking for a software that can estimate the difficulty of its synthesis and if possible the different synthetic routes, from commercial molecules. In my spare time I am working on a free and open source retrosynthesis reaction planner. However, I do not have enough time or experience to complete it on my own. I would welcome anyone who wants to help out and check out progress to contact me off-list or by phone. Thanks, - Bryan http://heybryan.org/ 1 512 203 0507http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--=_alternative 0029EF1FC125762B_= Content-Type: text/html; charset="US-ASCII"
Dear Bryan,

It is not free, but pretty good:

http://www.simbiosys.ca/archem/index.html

Regards,

Andras



"Bryan Bishop kanzure%x%gmail.com" <owner-chemistry^^^ccl.net>
Sent by: owner-chemistry+andras.borosy==givaudan.com^^^ccl.net

08.09.2009 02:31
Please respond to
"CCL Subscribers" <chemistry^^^ccl.net>
To
"Borosy, Andras " <andras.borosy^^^givaudan.com>
cc
Subject
CCL: Compound retrosynthesis






Sent to CCL by: Bryan Bishop [kanzure[*]gmail.com]
On Mon, Sep 7, 2009 at 4:10 PM, Werner K werner.schroedinger[*]gmail.com wrote:
> given a certain compound, for instance caffeina, I am looking for a software that can estimate the difficulty of its synthesis and if possible the different synthetic routes, from commercial molecules.

In my spare time I am working on a free and open source retrosynthesis
reaction planner. However, I do not have enough time or experience to
complete it on my own. I would welcome anyone who wants to help out
and check out progress to contact me off-list or by phone.

Thanks,

- Bryan
http://heybryan.org/
1 512 203 0507


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--=_alternative 0029EF1FC125762B_=-- From owner-chemistry@ccl.net Tue Sep 8 07:57:01 2009 From: "Hai-Bin Li lihb734::yahoo.com" To: CCL Subject: CCL:G: triplet excited states optimization in Gaussian03 Message-Id: <-40192-090908075519-6385-wOqHRelrpQaR0etPX1ZVlg[a]server.ccl.net> X-Original-From: "Hai-Bin Li" Date: Tue, 8 Sep 2009 07:55:16 -0400 Sent to CCL by: "Hai-Bin Li" [lihb734^yahoo.com] Dear CCL'users: I have a question to seek your advice in detail. If I want to optimize the first excited triplet state by CIS in Gaussian03, how should I set up the route line? I have several scheme as follows,can you give me some instuction? 1)using HF with spin Multiplicity = 3 #P hf/6-31g opt freq test test triplet using hf 0 3 O 0. 0. 0.05868 H 0. 1.19096 -0.23474 H 0. -1.19096 -0.23474 2)Using CIS and its option Triplet,BUT spin Multiplicity = 1, this method is RECOMMENED by my teachers? May you give a detailed reason? or what referecne should I refer to? #P CIS(TRIPLETS,ROOT=1)/6-31g opt freq test test triplet using hf 0 1 O 0. 0. 0.05868 H 0. 1.19096 -0.23474 H 0. -1.19096 -0.23474 3)Using CIS,BUT spin Multiplicity = 3 #P CIS(TRIPLETS,ROOT=1)/6-31g opt freq test test triplet using hf 0 3 O 0. 0. 0.05868 H 0. 1.19096 -0.23474 H 0. -1.19096 -0.23474 Thank you very much! Any comments and refercence is highly helpful. Best wishes. Haibin Li Institute of Functional Material Chemistry, Faculty of Chemistry Northeast Normal University changchun, Jilin, 130024 PR CHINA E-mail: lihb734 ~~ nenu.edu.cn; lihb734 ~~ yahoo.com http://www.nenu.edu.cn From owner-chemistry@ccl.net Tue Sep 8 09:12:01 2009 From: "Joaquin Barroso Flores joaco_barroso[*]yahoo.com" To: CCL Subject: CCL: Compound retrosynthesis Message-Id: <-40193-090908085743-5404-oXcxw6TW29Hpa6HCeTHAWA===server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-461306687-1252411050=:28281" Date: Tue, 8 Sep 2009 04:57:30 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso!^!yahoo.com] --0-461306687-1252411050=:28281 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable I remember such program was the BSc thesis of a classmate of mine back at U= NAM in Mexico, about a decade ago. Try to get in touch with Dr. Ivan Tubert= -Brohman, he might still have the perl code. He is easy to find through Goo= gle so you shouldn't have a problem getting in touch with him.=20 On a different topic; I would like to encourage everyone on the list to rec= over what to me seems to be a lost practice on CCL, which is posting summar= ies to answers received.=20 Cheers =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D =0AJoaquin Barroso-Flores, Ph. D. =0AFacultatea de Chimie, Universitatea Babes-Bolyai =0ACluj-Napoca, Romania =0A =0A -> http://joaquinbarroso.com =0A -> http://joaquinbarroso.wordpress.com =0A =0Ajoaquinbarroso''a''chem.ubbcluj.ro =0Ajoaquin.barroso''a''gmail.com=20 =0A =0A"Blogastronom=EDa": http://joaquinbarroso.blogspot.com=20 =0A=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D --- El lun 7-sep-09, Werner K werner.schroedinger:googlemail.com escribi=F3: De:: Werner K werner.schroedinger:googlemail.com Asunto: CCL: Compound retrosynthesis A: "Flores, Joaquin Barroso " Fecha: lunes 7 de septiembre de 2009, 16:10 Sent to CCL by: "Werner=A0 K" [werner.schroedinger..googlemail.com] Hi, given a certain compound, for instance caffeina, I am looking for a softwar= e that can estimate the difficulty of its synthesis and if possible the dif= ferent synthetic routes, from commercial molecules. Thanks -=3D This is automatically added to each message by the mailing script =3D-=A0 =A0 =A0=A0 =A0 =A0Subscribe/Unsubscribe:=20 =A0 =A0 =A0Job: http://www.ccl.net/jobs=20=A0 =A0 =A0=0A=0A=0A Encuentra las mejores recetas en Yahoo! Cocina. = =0Ahttp://mx.mujer.yahoo.com/cocina/ --0-461306687-1252411050=:28281 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
I remember such program was the BSc thesis of= a classmate of mine back at UNAM in Mexico, about a decade ago. Try to get= in touch with Dr. Ivan Tubert-Brohman, he might still have the perl code. = He is easy to find through Google so you shouldn't have a problem getting i= n touch with him.

On a different topic; I would like to encourage e= veryone on the list to recover what to me seems to be a lost practice on CC= L, which is posting summaries to answers received.

Cheers

= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D
=0AJoaquin Barroso-Flores, Ph. D.
=0AFacultatea de Chimie, Uni= versitatea Babes-Bolyai
=0ACluj-Napoca, Romania
=0A
=0A -> http= ://joaquinbarroso.com
=0A -> http://joaquinbarroso.wordpress.com
= =0A
=0Ajoaquinbarroso''a''chem.ubbcluj.ro
=0Ajoaquin.barroso''a''gmai= l.com
=0A
=0A"Blogastronom=EDa": http://joaquinbarroso.blogspot.com =
=0A=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D

--- El lun 7-sep-09, Werner K werner.schroedinger= :googlemail.com <owner-chemistry() ccl.net> escribi=F3:
<= blockquote style=3D"border-left: 2px solid rgb(16, 16, 255); margin-left: 5= px; padding-left: 5px;">
De:: Werner K werner.schroedinger:googlemail.co= m <owner-chemistry() ccl.net>
Asunto: CCL: Compound retrosynthesisA: "Flores, Joaquin Barroso " <joaco_barroso() yahoo.com>
= Fecha: lunes 7 de septiembre de 2009, 16:10


Sent to CCL by: "Werner  K" [werner.schroedinger..googlemail.com]=
Hi,

given a certain compound, for instance caffeina, I am lookin= g for a software that can estimate the difficulty of its synthesis and if p= ossible the different synthetic routes, from commercial molecules.

T= hanks



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=0A=0A=0A=0A

=A1Encuentra las mejores recetas
con Yahoo! Cocina!
= =0Ahttp://mx.mujer.yahoo.com/cocina/ --0-461306687-1252411050=:28281-- From owner-chemistry@ccl.net Tue Sep 8 11:00:01 2009 From: "Aniko Simon aniko===simbiosys.ca" To: CCL Subject: CCL: Compound retrosynthesis Message-Id: <-40194-090908104843-11625-iA0gUcbe9Ggzkc2J7w6ojg*server.ccl.net> X-Original-From: "Aniko Simon" Date: Tue, 8 Sep 2009 10:48:40 -0400 Sent to CCL by: "Aniko Simon" [aniko%x%simbiosys.ca] Dear All, In addition to the URL that Andras mentioned below, I would like to highlight the publication page for ARChem: http://www.simbiosys.ca/archem/archem_publications.html The paper describing ARChem contains an elaborate overview of the field and may lead you to other relevant tools: J Law et.al: Route Designer: A Retrosynthetic Analysis Tool Utilizing Automated Retrosynthetic Rule Generation J Chem Inf Model. 2009 Mar;49(3):593-602. DOI: 10.1021/ci800228y http://pubs.acs.org/doi/abs/10.1021/ci800228y Some of our earlier- yet still popular- work in this domain is: CAESA for estimation of synthetic accessibility: http://www.simbiosys.ca/caesa/index.html Finally, the following article was one of the top 10 most accessed articles in J. Med Chem. in 2007. The theory in this paper has been implemented in Topoplex, a new tool which has been released very recently. K. Boda and A. P. Johnson: Molecular Complexity Analysis of de Novo Designed Ligands J. Med. Chem., 2006, 49 (20), pp 5869 - 5879 DOI: 10.1021/jm050054p http://pubs.acs.org/doi/abs/10.1021/jm050054p Hope this helps you find what you are looking for. best, Aniko On September 8, 2009, andras.borosy%x%givaudan.com wrote: > Dear Bryan, > > It is not free, but pretty good: > > http://www.simbiosys.ca/archem/index.html > > Regards, > > Andras > > > > > "Bryan Bishop kanzure%x%gmail.com" > Sent by: owner-chemistry+andras.borosy==givaudan.com|a|ccl.net > 08.09.2009 02:31 > Please respond to > "CCL Subscribers" > > > To > "Borosy, Andras " > cc > > Subject > CCL: Compound retrosynthesis > > > Sent to CCL by: Bryan Bishop [kanzure[*]gmail.com] > On Mon, Sep 7, 2009 at 4:10 PM, Werner K werner.schroedinger[*]gmail.com > > wrote: > > given a certain compound, for instance caffeina, I am looking for a > > software that can estimate the difficulty of its synthesis and if possible > the different synthetic routes, from commercial molecules. > > In my spare time I am working on a free and open source retrosynthesis > reaction planner. However, I do not have enough time or experience to > complete it on my own. I would welcome anyone who wants to help out > and check out progress to contact me off-list or by phone. > > Thanks, > > - Bryan > http://heybryan.org/ > 1 512 203 From owner-chemistry@ccl.net Tue Sep 8 16:59:01 2009 From: "Henry Martinez hmartine- -gmail.com" To: CCL Subject: CCL:G: Atoms repulsion calculation Message-Id: <-40195-090908165818-7000-JogCPQK5nTkootXxHc970g---server.ccl.net> X-Original-From: "Henry Martinez" Date: Tue, 8 Sep 2009 16:58:13 -0400 Sent to CCL by: "Henry Martinez" [hmartine.:.gmail.com] Hi, I am using Gaussian 03, and I would like to know if there is anyway I would be able to know if there is any repulsion interaction between two atoms of the same molecule that are close to each other. For being more specific, there is an internal cyclization reaction. The atom who attacks can do it from one angle or another, however after calculating the Transition state the angle of the attacker makes me think that there might be a repulsion interaction. How can I know this? Thanks a lot From owner-chemistry@ccl.net Tue Sep 8 23:38:00 2009 From: "Yves Wang yves.wang/./duke.edu" To: CCL Subject: CCL: PCM "not converged" error in GAMESS Message-Id: <-40196-090908233727-21262-hx4LfQuH6hy8o2OB5JKhww]_[server.ccl.net> X-Original-From: "Yves Wang" Date: Tue, 8 Sep 2009 23:37:24 -0400 Sent to CCL by: "Yves Wang" [yves.wang * duke.edu] Hi CCLers, I was running NBO calculations with PCM models in GAMESS. The SCF calculation in the NEDA analysis always gave me this message: ! ! ! ! WARNING ! ! ! ! PCM ITERATIVE PROCEDURE NOT CONVERGED IN 50 ITERATIONS GAMESS WILL PROCEED DESPITE THIS ... and the results were way off. What confuses me is I have set the maximum number of PCM iterations to 200. (at least I think I have). And the PCM still stopped at 50 iterations. Here is my input card: $CONTRL RUNTYP=Energy DFTTYP=B3LYP MAXIT=200 $END $CONTRL SCFTYP=RHF $END $BASIS GBASIS=ACCT $END $SYSTEM MWORDS=50 $END $CONTRL NOSYM=1 $END $PCM SOLVNT=WATER IEF=-10 $END $PCMITR MAXITR1=200 MAXITR2=200 MAXDIIS=200 $END $NBO STERIC DIPOLE $END $DEL NEDA END $END $DATA Any suggestion is gratefully appreciated. Yves