From owner-chemistry@ccl.net Thu Nov 12 00:00:00 2009 From: "yvonne Connolly Martin yvonnecmartin^^^gmail.com" To: CCL Subject: CCL: Removing salts Message-Id: <-40666-091111224556-3333-rsHEOiLM8Kroy5ID8Dt9Uw##server.ccl.net> X-Original-From: "yvonne Connolly Martin" Date: Wed, 11 Nov 2009 22:45:52 -0500 Sent to CCL by: "yvonne Connolly Martin" [yvonnecmartin^gmail.com] Although removing the smallest part of a salt is a common strategy, it can produce unwanted results if the removed portion is actually the biologically active one. If you can convert the desalted structures to canonical SMILES or InChI, then it is easy to find the duplicates and trace back to the salts that need more attention. You might be surprised to see how many benzene sulfonic acid salts are in your database! From owner-chemistry@ccl.net Thu Nov 12 00:36:01 2009 From: "Gang Lv yoghurt117(-)yahoo.com.cn" To: CCL Subject: CCL: Use Gamess with the atoms in molecules wavefunction computation Message-Id: <-40667-091111084445-11067-DqdveY7D7AWtyZekbSnvtA%a%server.ccl.net> X-Original-From: "Gang Lv" Date: Wed, 11 Nov 2009 08:44:41 -0500 Sent to CCL by: "Gang Lv" [yoghurt117++yahoo.com.cn] I have computated the molecule with the AIMPAC=.true. and the RUNTYP=ENERGY in $CONTRL part, with MP2 method. And the $MP2 MP2PRP=.TRUE. $END is added. Part of the input file is as follow: $CONTRL SCFTYP=RHF RUNTYP=PROP MPLEVL=2 MAXIT=30 MULT=1 AIMPAC=.TRUE. RUNTYP=ENERGY $END $SYSTEM TIMLIM=525600 MEMORY=52428800 $END $BASIS GBASIS=N21 NGAUSS=3 $END $SCF DIRSCF=.TRUE. $END $MP2 MP2PRP=.TRUE. $END $DATA Then after finished the computation, I found three files in the 'temp' directry, i.e, an *.dat, an *.F09 and an *.F16. My question is how to produce the *.wfn file. And another is how to produce the wfn file if I use DFT method. Thank you! From owner-chemistry@ccl.net Thu Nov 12 01:10:01 2009 From: "Indra Neela Y indraneelaroy * gmail.com" To: CCL Subject: CCL: Request for Ice Ih crystal structure Message-Id: <-40668-091111041526-16082-TB9V2vmzotPa2UZSNkMVPA^server.ccl.net> X-Original-From: "Indra Neela Y" Date: Wed, 11 Nov 2009 04:15:21 -0500 Sent to CCL by: "Indra Neela Y" [indraneelaroy ~~ gmail.com] I am looking for XYZ coordinates (in angstroms) of Ice XI (hexamer chair conformation stacks) and Ice Ih crystal structures, if anyone of you have it kindly provide me. Thanks and regards, Indra Neela. Y indraneelaroy^^gmail.com From owner-chemistry@ccl.net Thu Nov 12 01:51:00 2009 From: "Christoph Allolio Christoph.Allolio|*|mailbox.tu-dresden.de" To: CCL Subject: CCL: remove salts from compounds Message-Id: <-40669-091110172340-29392-60REzAKj9wv0veQ3AQGu0A#server.ccl.net> X-Original-From: Christoph Allolio Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Date: Tue, 10 Nov 2009 22:51:11 +0100 MIME-Version: 1.0 Sent to CCL by: Christoph Allolio [Christoph.Allolio]_[mailbox.tu-dresden.de] Zitat von "amit dong dongamit123a/gmail.com" : > Hi, > > Is there any free tool that can be used for removing ions/salts from a large > library of compounds? > > Thanks > AD > Hi Amit You may use the OpenBabel API (GPL), which has a StripSalts functionality. The molecule may be loaded for example from a SMILES string. It however only strips a disconnected fragment of a size smaller than a specified number of atoms. This can be implemented within a few lines of code and is suitably fast for several tens of thousands of molecules to be processed within a few minutes. If there is a better free way i'd like to know it too. Regards Christoph Allolio From owner-chemistry@ccl.net Thu Nov 12 03:47:00 2009 From: "neeraj misra neerajmisra.:.hotmail.com" To: CCL Subject: CCL: GVIEW Message-Id: <-40670-091112015156-15928-gOj10RHV9tZ2TWi9MXu0wA a server.ccl.net> X-Original-From: "neeraj misra" Date: Thu, 12 Nov 2009 01:51:52 -0500 Sent to CCL by: "neeraj misra" [neerajmisra|,|hotmail.com] HOW TO SAVE THE IMAGE OF HOMO-LUMO FROM GAUSSVIEW? From owner-chemistry@ccl.net Thu Nov 12 06:03:00 2009 From: "Werner K werner.schroedinger[*]googlemail.com" To: CCL Subject: CCL: Docking simulations with a salt bridge Message-Id: <-40671-091112060149-16205-yFp4oqOFGPa1RbDFWoey0A(_)server.ccl.net> X-Original-From: "Werner K" Date: Thu, 12 Nov 2009 06:01:46 -0500 Sent to CCL by: "Werner K" [werner.schroedinger++googlemail.com] Hi, there is a receptor, which has a salt bridge. When a ligand interacts with it, and breaks the salt bridge, the receptor is activated in another part of the molecule. I wonder what simulation-approach/software/ideas would you recommend to use that can deal with docking ligands and breaking salt bridges. Thanks WS From owner-chemistry@ccl.net Thu Nov 12 06:37:01 2009 From: "Jens Spanget-Larsen spanget^_^ruc.dk" To: CCL Subject: CCL:G: Gaussian ZINDO ground state Message-Id: <-40672-091112061403-20950-R17FX30mhgMTYdONdglFaQ..server.ccl.net> X-Original-From: Jens Spanget-Larsen Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 12 Nov 2009 11:17:28 +0100 MIME-Version: 1.0 Sent to CCL by: Jens Spanget-Larsen [spanget_-_ruc.dk] Dear Bahman, the ZINDO-CIS ground state is identical to the SCF ground state. According to the Brillouin theorem, singly excited electronic configurations do not interact with the Hartree-Fock-SCF ground configuration. Doubly and higher excited configurations may mix with the ground configuration and lower the calculated ground state energy; this amounts to a consideration of electronic correlation effects. Yours, Jens >--< ------------------------------------------------------ JENS SPANGET-LARSEN Office: +45 4674 2710 Dept. of Science (18.1) Fax: +45 4674 3011 Roskilde University Mobile: +45 2320 6246 P.O.Box 260 E-Mail: spanget**ruc.dk DK-4000 Roskilde, Denmark http://www.ruc.dk/~spanget ------------------------------------------------------ Bahman Roostaei bahman.roostaei|a|utsa.edu wrote: > Sent to CCL by: "Bahman Roostaei" [bahman.roostaei,,utsa.edu] > Hi everybody, > > As a newly entered individual into this field, I am trying to clear out some > concepts for myself. My confusion is in Gaussian Zindo. The Gaussian Zindo > includes some sort of CI calculation. Why Gaussian does not report the CI > coefficients for the first eigenstate of the CI Hamiltonian ? it always starts > with reporting the CI coefficients of the first excited state. am I missing > something here ? is it because the ground state of the Zindo-CI is the same as > HF ground state ? If that's true why the SCF density is not diagonalized in the > output? > > Thanks. > Bahman.> > > From owner-chemistry@ccl.net Thu Nov 12 07:14:00 2009 From: "Joaquin Barroso Flores joaco_barroso]~[yahoo.com" To: CCL Subject: CCL:G: Electrostatic potential surface from NBO Message-Id: <-40673-091112052616-13599-t1uZdSO0CsIK+f2PnulNXQ-$-server.ccl.net> X-Original-From: Joaquin Barroso Flores Content-Type: multipart/alternative; boundary="0-997599064-1258021564=:65330" Date: Thu, 12 Nov 2009 02:26:04 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Joaquin Barroso Flores [joaco_barroso:+:yahoo.com] --0-997599064-1258021564=:65330 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi=0A=0AOne way would be "tricking" Molekel into reading them by copy-pasti= ng those charges on top the Mulliken charges of a 'gaussian-like' output fi= le.=0AFind the last string in your output file, that says "Mulliken atomic = charges" in G03 or "Total atomic charges" in G98 (if the former one is the = case, and your molekel version is 3.x (i.e. prior to 5.x), then you have to= change "Mulliken" for "Total"). =0ARemember the G03 headline must be repl= aced by G98 (famous molekel 3.x bug)=0A=0ANow, if you got NBO 5.0, didn't y= ou get NBO view as well? I haven't used it (YET), but i guess it should be = able to do what you need. =0A=0AGreetings=0A=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=0AJoaquin Barroso-Flore= s, Ph. D.=0AFacultatea de Chimie, Universitatea Babes-Bolyai=0ACluj-Napoca,= Romania=0A=0A=0A-> http://joaquinbarroso[dot]com=0A-> http://joaquinbarros= o[dot]wordpress[dot]com=0A=0Ajoaquinbarroso''a''chem[dot]ubbcluj[dot]ro=0Aj= oaquin.barroso''a''gmail[dot]com =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=0A=0A=0A=0A=0A=0A__________________= ______________=0ADe: Yves Wang yves.wang^duke.edu = =0APara: "Flores, Joaquin Barroso " =0AEnv= iado: mi=E9, noviembre 11, 2009 11:00:35 PM=0AAsunto: CCL: Electrostatic po= tential surface from NBO=0A=0A=0ASent to CCL by: Yves Wang [yves.wang*duke.= edu]=0ADavid Eisenberg david.eisen(0)gmail.com wrote:=0A> Sent to CCL by: "= David Eisenberg" [david.eisen]![gmail.com]=0A> Dear CCL community,=0A> =0A= > Is there a way of displaying an electrostatic potential surface of a mole= cule, based on a NBO charge distribution calculation?=0A> =0A> I have Chem3= D and Molekel, and NBO 5.0.=0A> =0A> Thanks,=0A> David Eisenberg=0A> Jerusa= lem>=0A> =0A> =0AHi David,=0A=0AIt seems to me that NBO only gives you par= tial charges on atoms, i.e. the Natural Population Analysis. I believe ther= e should be some software that can determine the potential surface based on= partial charges. It should be irrelevant NBO.=0A=0ABest,=0A=0A-- Yi(Yves) = Wang=0ADepartment of Biochemistry=0AStructural Biology & Biophysics Program= =0ADuke University=0ABS: University of Science and Technology of China=0ASc= hool of Life Sciences, National Laboratory for Physical Sciences=0A at M= icroscale=0ATel: +1-919-236-3307 (Cell)=0A +1-919-684-0235 (Lab 1)=0A = +1-919-660-1634 (Lab 2)=0AOffice: A20 LSRC / 5301 FFSC=0AE-Mail: yves.wang= -,-duke.edu=0AMail: Box 90317, Chemistry Department=0A=0A=0A=0A-=3D This is= automatically added to each message by the mailing script =3D-=0ATo recove= r the email address of the author of the message, please change=0Athe stran= ge characters on the top line to the _ sign. You can also=0Alook up the X-O= riginal-From: line in the mail header.=0A=0AE-mail to subscribers: CHEMISTR= Y _ ccl.net or use:=0A=0A= =0A=0A http://= www.ccl.net/cgi-bin/ccl/send_ccl_message=0A=0Ah= ttp://www.ccl.net/chemistry/sub_unsub.shtml=0A=0ABefore posting, check wait= time at: http://www.ccl.net=0A=0AConferences:= http://server.ccl.net/chemistry/announcements/conferences/=0A=0ASearch Mes= sages: http://www.ccl.net/chemistry/searchccl/index.shtml=0A=0AIf your mail= bounces from CCL with 5.7.1 error, check:=0A http://www.ccl.net/spammer= s.txt=0A=0A=0A=0A= =0A Encuentra las mejores recetas en Yahoo! Cocina. = =0Ahttp://mx.mujer.yahoo.com/cocina/ --0-997599064-1258021564=:65330 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi

One way would be "tricking" Molekel into reading the= m by copy-pasting those charges on top the Mulliken charges of a 'gaussian-= like' output file.
Find the last string in your output file, that says "= Mulliken atomic charges" in G03 or "Total atomic charges" in G98 (if the fo= rmer one is the case, and your molekel version is 3.x (i.e. prior to 5.x), = then you have to change "Mulliken" for "Total"). 
Remember the G03= headline must be replaced by G98 (famous molekel 3.x bug)

Now, if y= ou got NBO 5.0, didn't you get NBO view as well? I haven't used it (YET), b= ut i guess it should be able to do what you need.

Greetings

= =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
Joaquin Barroso-Flores, Ph. D.
Facultatea de Chimie, Universitate= a Babes-Bolyai
Cluj-Napoca, Romania


joaquinbarroso''a''chem[dot]ubbcluj[dot]ro
joaqui= n.barroso''a''gmail[dot]com
=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


<= div style=3D"font-family: arial,helvetica,sans-serif; font-size: 10pt;">
De: Yves Wang yves.wang^duke.edu <owner-chemistry _ ccl= .net>
Para: "Flores,= Joaquin Barroso " <joaco_barroso _ yahoo.com>
Enviado: mi=E9, noviembre 11, 2009 11:00:35 PM
Asunto: CCL: Electrostatic potential surface from NBO


Sent to CCL by: Yves Wang [yves.wang*duke.edu]
David Eisenb= erg david.eisen(0)gmail.com wrote:
> Sent to CCL by: "David  Eis= enberg" [david.eisen]![gmail.com]
> Dear CCL community,
>
&= gt; Is there a way of displaying an electrostatic potential surface of a mo= lecule, based on a NBO charge distribution calculation?
>
> I = have Chem3D and Molekel, and NBO 5.0.
>
> Thanks,
> Davi= d Eisenberg
> Jerusalem>
>
> 
Hi David,
=
It seems to me that NBO only gives you partial charges on atoms, i.e. t= he Natural Population Analysis. I believe there should be some software tha= t can determine the potential surface based on partial charges. It should b= e irrelevant NBO.

Best,

-- Yi(Yves) Wang
Department of Biochemistry
Structural Biology & Biophysics Program
Duke Univer= sity
BS: University of Science and Technology of China
School of Life= Sciences, National Laboratory for Physical Sciences
    = at Microscale
Tel: +1-919-236-3307 (Cell)
    +1-919-684-02= 35 (Lab 1)
    +1-919-660-1634 (Lab 2)
Office: A20 LSRC / 5= 301 FFSC
E-Mail: yves.wang-,-duke.edu
Mail: Box 90317, Chemistry Depa= rtment



-=3D This is automatically added to each message by t= he mailing script =3D-
To recover the email address of the author of the= message, please change
the strange characters on the top line to the _ = sign. You can also
E-mail to subscribers: CHEMISTRY _ ccl.net or use:
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RTFI: http://www.ccl.net/chemistry/aboutccl/instr= uctions/


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

=A1Encuentra las mejore= s recetas
con Yahoo! Cocina!
=0Ahttp://mx.mujer.yahoo.com/cocina/ --0-997599064-1258021564=:65330-- From owner-chemistry@ccl.net Thu Nov 12 09:19:01 2009 From: "Stephen Bowlus chezbowlus###comcast.net" To: CCL Subject: CCL: remove salts from compounds Message-Id: <-40674-091112091022-12426-Tb3yxJhXmiDvgMcwwE9yPw(_)server.ccl.net> X-Original-From: Stephen Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Thu, 12 Nov 2009 06:10:01 -0800 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Stephen Bowlus [chezbowlus|-|comcast.net] >> Hi, >> >> Is there any free tool that can be used for removing ions/salts >> from a large >> library of compounds? >> >> Thanks >> AD >> Look at MayaChemTools.org. There is a switch in the filterSDfiles script for washing salts from SD files (largest fragment kept). -sb From owner-chemistry@ccl.net Thu Nov 12 09:54:01 2009 From: "Serghei Glinca glinca\a/staff.uni-marburg.de" To: CCL Subject: CCL: =?windows-1252?Q?Announcement_=22The_Interactome=3A_From_?= =?windows-1252?Q?Atom-Atom_Contacts_to_Networks_in_Systems_B?= =?windows-1252?Q?iology=94=2C_Workshop_Rauischholzhausen=2C_March_?= =?windows-1252?Q?22-25=2C_2010?= Message-Id: <-40675-091112094124-24791-F9VdfwPh6YcOW7NbzhF3MQ*o*server.ccl.net> X-Original-From: Serghei Glinca Content-Type: multipart/alternative; boundary="------------080100040202050503010009" Date: Thu, 12 Nov 2009 15:11:37 +0100 MIME-Version: 1.0 Sent to CCL by: Serghei Glinca [glinca::staff.uni-marburg.de] This is a multi-part message in MIME format. --------------080100040202050503010009 Content-Type: text/plain; charset=windows-1252; format=flowed Content-Transfer-Encoding: 8bit Dear colleagues, We want to announce the sixth workshop on *"New Approaches in Drug Design and Discovery"* to be hold next year, in March 22-25, 2010 in Rauischholzhausen, Germany. Over the last years we have successfully established a series of workshops with biannual frequency, and we would like to organize the next workshop on the special topic: *"The Interactome: From Atom-Atom Contacts to Networks in Systems Biology”* This topic will cover the latest developments in the field of drug discovery taking the increasing expertise about networking among proteins in cellular processes into consideration. What can systems biology contribute to our field of research? Can we expect important insights into the mode of action of drugs, particularly with respect to “poly-pharmacology”? Nevertheless, we do not want to loose the sight on molecular aspects of our field of interest. Therefore, we want to start > from atomic details of interactions as captured by quantum chemistry and proceed via computational tools that support the design and ranking of our hypotheses. The meeting will also cover latest developments in some special target classes such as kinases and P450 enzymes. What can chemical biology contribute to screening, target discovery, and lead discovery? Such techniques are also of utmost importance in the characterization of protein networking in cells. How much can computational tools support the identification of proteins that mutually talk to each other in signalling cascades? Do not miss to reserve early on your participation in this meeting. You can apply under: http://www.agklebe.de/workshop2010 The workshop is organized by: * Gerhard Klebe (Institute of Pharmaceutical Chemistry , Univ. of Marburg) * Hans Matter (Sanofi-Aventis, Chemical Sciences - Drug Design , Frankfurt) * Christoph Sotriffer (Institute of Pharmacy ,Univ. of Wuerzburg) / per pro, Serghei Glinca/ -- Serghei Glinca Group of Prof. Dr. G. Klebe Department of Pharmaceutical Chemistry University of Marburg Marbacher Weg 6 D-35032 Marburg, Germany Phone: +49 6421 28-21339 Email: serghei.glinca|staff.uni-marburg.de www.agklebe.de --------------080100040202050503010009 Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: 8bit

Dear colleagues,

We want to announce the sixth workshop on 
"New Approaches in Drug Design and Discovery"
to be hold next year, in March 22-25, 2010 in Rauischholzhausen, Germany.
Over the last years we have successfully established a series of workshops with biannual frequency, 
and we would like to organize the next workshop on the special topic:
"The Interactome: From Atom-Atom Contacts to Networks in Systems Biology”

This topic will cover the latest developments in the field of drug discovery taking the increasing expertise about networking among proteins in cellular processes into consideration. What can systems biology contribute to our field of research? Can we expect important insights into the mode of action of drugs, particularly with respect to “poly-pharmacology”? Nevertheless, we do not want to loose the sight on molecular aspects of our field of interest. Therefore, we want to start from atomic details of interactions as captured by quantum chemistry and proceed via computational tools that support the design and ranking of our hypotheses. The meeting will also cover latest developments in some special target classes such as kinases and P450 enzymes. What can chemical biology contribute to screening, target discovery, and lead discovery? Such techniques are also of utmost importance in the characterization of protein networking in cells. How much can computational tools support the identification of proteins that mutually talk to each other in signalling cascades?

Do not miss to reserve early on your participation in this meeting. You can apply under:

http://www.agklebe.de/workshop2010

The workshop is organized by:




per pro,

Serghei Glinca
-- 
Serghei Glinca
Group of Prof. Dr. G. Klebe
Department of Pharmaceutical Chemistry
University of Marburg
Marbacher Weg 6
D-35032 Marburg, Germany

Phone: +49 6421 28-21339
Email: serghei.glinca|staff.uni-marburg.de
www.agklebe.de
--------------080100040202050503010009-- From owner-chemistry@ccl.net Thu Nov 12 22:50:01 2009 From: "YZ Lan lyzhao*zjnu.cn" To: CCL Subject: CCL: Two questions about the nonlinear optical properties. Message-Id: <-40676-091112221908-5931-ByZRxb0LlYXV2Zh4I732lA(!)server.ccl.net> X-Original-From: "YZ Lan" Date: Thu, 12 Nov 2009 22:19:02 -0500 Sent to CCL by: "YZ Lan" [lyzhao**zjnu.cn] Dear CCLer, 1, Is the sign of the (hyper)polarizability related to the definition of coordinate direction of a molecule? 2, Multiphoton absorption means a material can absorb multiphotons (i.e. n(hv)) simultaneously. How to understand the Einstein formula: hv=(1/2)mv^2+W, that is, is this formula possibly changed to n(hv)=(1/2)mv^2+W? Could you give me some references? Great thanks for any helps! Lan