From owner-chemistry@ccl.net Fri Nov 25 00:23:01 2005 From: "Kim Hanjo lordmiss%x%gmail.com" To: CCL Subject: CCL: seek software about "rule 5" Message-Id: <-30064-051124203619-10781-4rueGL44kDMmBcaj4lb2XA+*+server.ccl.net> X-Original-From: Kim Hanjo Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 25 Nov 2005 09:35:53 +0900 MIME-Version: 1.0 Sent to CCL by: Kim Hanjo [lordmiss*|*gmail.com] You can do it in this homepage; http://preadmet.bmdrc.org After free register, you can calculate more than 900 descriptors, use drug-likeness filters, and predict ADME properties. Cheers! -------------------------------------------------------------------- Kim Hanjo Ph. D. Drug Discovery Division, Research Institute of Bioinformatics & Molecular Design B138A Yonsei Engineering Research Complex, Yonsei University Seoul 120-749, Korea. http://www.hanjo.pe.kr Tel) +82-2-393-9551 ex) 206 Fax) +82-2-393-9554 E-mail) lordmiss#chol.com, lordmiss#bmdrc.org -------------------------------------------------------------------- yzhao yzhao,mail.sioc.ac.cn wrote: > Sent to CCL by: "yzhao" [yzhao..mail.sioc.ac.cn] > > --------------Boundary-00=_TFOE6RO0000000000000 > Content-Type: Text/Plain; > charset="gb2312" > Content-Transfer-Encoding: quoted-printable > > Hi, cclers!=0D > =0D > I'm trying to utilize "rule 5" to filter molecules from a large databas= > e. > Can anybody tell me where to find some existing program or software that = > can > do these jobs?=0D > Thanks in advance!=0D > =0D > Steven > --------------Boundary-00=_TFOE6RO0000000000000 > Content-Type: Text/HTML; > charset="gb2312" > Content-Transfer-Encoding: quoted-printable > > > > > > > 10px 10px; FONT-FAMILY: Arial" bgColor=3D#ffffff background=3D"" scroll=3D= > yes ORGYPOS=3D"0"> > %" border=3D0> > > > > >

AMILY: Arial" width=3D"100%"> >

Hi, cclers!

I'm trying to utilize "rule 5" to filter molecules from = > a large database. Can anybody tell me where to find some existing pr= > ogram or software that can do these jobs?

Thanks in advance!

Steven

> > > > > > ABLE>

> --------------Boundary-00=_TFOE6RO0000000000000--> > > > > From owner-chemistry@ccl.net Fri Nov 25 10:26:00 2005 From: "Jim Kress ccl_nospam]^[kressworks.com" To: CCL Subject: CCL: COSMOtherm / COSMO-RS training courses Message-Id: <-30065-051125101945-9546-d1HXiXH0+DYqRtaHFu8wjA++server.ccl.net> X-Original-From: "Jim Kress" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 25 Nov 2005 10:19:10 -0500 MIME-Version: 1.0 Sent to CCL by: "Jim Kress" [ccl_nospam=-=kressworks.com] Why don't you do these courses as webinars like Schrödinger Software? Jim > -----Original Message----- > From: Karin Wichmann wichmann:_:cosmologic.de > [mailto:owner-chemistry_._ccl.net] > Sent: Thursday, November 24, 2005 12:04 PM > To: Kress, Jim > Subject: CCL: COSMOtherm / COSMO-RS training courses > > Sent to CCL by: Karin Wichmann [wichmann : cosmologic.de] > COSMOlogic has a small number of seats available for free > COSMOtherm training courses on Dec 5, 12 and 13. These are > one-day courses covering COSMO-RS theory for fluid > thermodynamics and its applications in the areas of chemical > engineering and life science. The courses will take place at > our location in Leverkusen (Germany). > > For further information please contact us at cosmotherm (AT) > cosmologic.de > > -- > ----------------------------------- > Dr. Karin Wichmann > COSMOlogic GmbH & Co. KG > Burscheider Str. 515 > D-51381 Leverkusen > Germany > > Phone +49-2171-73168-4 > Fax +49-2171-73168-9 > Email wichmann (AT) cosmologic.de > Web http://www.cosmologic.de > ----------------------------------- > > > > -= 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.> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > From owner-chemistry@ccl.net Fri Nov 25 11:00:01 2005 From: "ragubalaji n ragubalaji_._gmail.com" To: CCL Subject: CCL: STRUCTURES TO SMILES Message-Id: <-30066-051125024012-6040-6dnlDDGNaP9xBOCQlmcxng,server.ccl.net> X-Original-From: "ragubalaji n" Sent to CCL by: "ragubalaji n" [ragubalaji::gmail.com] Hi all, I am looking for tool where SMILES strings can be generated from structures or connectivity tables. Could anybody tell me where I can find it? Thank you very much. ragu Bangalore ragubalaji.,.gmail.com From owner-chemistry@ccl.net Fri Nov 25 11:35:01 2005 From: "Andrew Fant fant ~~ pobox.com" To: CCL Subject: CCL: Public HTS screening data Message-Id: <-30067-051125063615-7423-TTv3DcpCgZwBb8M8qdVVzQ a server.ccl.net> X-Original-From: Andrew Fant Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 23 Nov 2005 12:28:56 -0500 MIME-Version: 1.0 Sent to CCL by: Andrew Fant [fant^_^pobox.com] Michael K. Gilson gilson%a%umbi.umd.edu wrote: > Sent to CCL by: "Michael K. Gilson" [gilson_+_umbi.umd.edu] > BindingDB now allows SDfile downloads of compounds and inhibition > constants for a given target. I'm not sure if this is exactly what you > are after, though, since these are not HTS sets. On the other hand, some > targets have hundreds of compounds. > > You might also want to look at what is available now at PubChem. > > Regards, > Mike > > Kim Branson kim.branson++gmail.com wrote: > > >>Sent to CCL by: Kim Branson [kim.branson%x%gmail.com] >>-----BEGIN PGP SIGNED MESSAGE----- >>Hash: SHA1 >> >> >>Hi all, >> >>i'm looking for public HTS screening datasets that I can use to compare >>docking and scoring methods against. Naturally a structure of the >>target must be accessible, with the compounds in the screening >>library. I have the McMasters sets, and I am aware of efforts like >>chembank, however getting the structures from the database is >>problematic. If anyone can point me at other sets, or can possibly >>collaborate i'd be grateful. >> >>I'd also like any examples of failed HTS screens, where no "real hits" >>were found. I think this might prove to be an excellent control for >>these types of comparisons. >> >>cheers >> >>kim Kim, You also might want to check the HTS group at McMaster University in Hamilton. They sponsored a competition on HTS data mining this past year. The web site can be found at http://hts.mcmaster.ca/HTSDataMiningCompetition.htm . The data set was entirely based on DHFR inhibition, but it included several novel inhibitors and the results of the screens they used as the basis of the competition are now in the literature. Hopefully this will be a regular sort of contest from various research groups and we will be able to get a "bake-off" of methods in virtual screening and HTS analysis going on a regular basis. Andy From owner-chemistry@ccl.net Fri Nov 25 12:34:00 2005 From: "Tomasz Grabarkiewicz grabar a man.poznan.pl" To: CCL Subject: CCL: Help with CSMs of salt solutions needed Message-Id: <-30068-051125121517-3819-ZHHJcmgC3+9rAcbpENCHvg .. server.ccl.net> X-Original-From: "Tomasz Grabarkiewicz" Content-Type: multipart/alternative; boundary="----=_NextPart_000_0037_01C5F1E5.AEF42D90" Date: Fri, 25 Nov 2005 17:28:43 +0100 MIME-Version: 1.0 Sent to CCL by: "Tomasz Grabarkiewicz" [grabar]*[man.poznan.pl] This is a multi-part message in MIME format. ------=_NextPart_000_0037_01C5F1E5.AEF42D90 Content-Type: text/plain; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable Hi CCLers, Does anyone of you have any experience in dealing with a continuum = solvation models of salt solutions? I'm interested in how the salt = concentration affects the dynamics of a certain process. I'd like to = perform a series of calculations in different concentrations. Unfortunately I have no idea what value of the dielectric constant = should be assigned in each case. I searched through the internet but didn't find anything appropriate = besides this (Hasted, J. B., Ritson, D. M. and Collie, C. H. (1948). = "Dielectric Properties of Aqueous Ionic Solutions. Parts I and II," The = Journal of Chemical Physics, vol 16, No.1. - but have no access to it) Can anyone help me? Thanks, Tomasz ------=_NextPart_000_0037_01C5F1E5.AEF42D90 Content-Type: text/html; charset="iso-8859-2" Content-Transfer-Encoding: quoted-printable

Hi CCLers,

Does anyone of you have any experience in dealing with a continuum=20 solvation models of salt solutions? I'm interested in how the salt = concentration=20 affects the dynamics of a certain process. I'd like to perform a series = of=20 calculations in different concentrations.

Unfortunately I have no idea what value of the dielectric = constant=20 should be assigned in each case.

I searched through the internet but didn't find anything = appropriate=20 besides this (Hasted, J. B., Ritson, D. M. and Collie, C. H. (1948). = "Dielectric=20 Properties of Aqueous Ionic Solutions. Parts I and II," The Journal = of=20 Chemical Physics, vol 16, No.1. - but have no access to it)

Can anyone help me?

Thanks,

Tomasz

------=_NextPart_000_0037_01C5F1E5.AEF42D90-- From owner-chemistry@ccl.net Fri Nov 25 13:35:00 2005 From: "David F. Green dfgreen[]ams.sunysb.edu" To: CCL Subject: CCL: Help with CSMs of salt solutions needed Message-Id: <-30069-051125133306-13088-DFeECIbjLmOglzDr6tBeVQ|a|server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 25 Nov 2005 13:32:50 -0500 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen(~)ams.sunysb.edu] Tomasz, Salt-concentration effects do not factor into the dielectric constant. Rather, generally a Debye-Huckel treatment of mobile ions is used, with the ionic strength being the relavent parameter. This added consideration of salt is what separates a Poisson-Boltzman treatment > from a simple Poisson equation description, and most Generalized Born models have incorporated a similar treatment. As far as I am aware, most packages capabable of continuum electrostatic calculations include an ability to treat salt in this manner. Depending on the nature of the system you are considering, you should be aware that many implementations only allow for monovalent ions to be considered, and others may be additionally be based on the linearized Poisson-Boltzman equation, rather than the non-linear form. For more information, do a literature search on "Poisson-Boltzmann", "Generalized-Born" and "Self-Consistent Reaction Field" (the latter if you are working with QM models rather thatn MM). "An Introduction to Statistical Thermodynamics" by T.L. Hill also has pretty good treatment of the background theory -- and the Dover paperback is only ~$12. Cheers, David ======================================================================== David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Office: +1-631-632-9344 Math Tower, Room 1-117 Mobile: +1-617-953-3922 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================== Tomasz Grabarkiewicz grabar a man.poznan.pl wrote: > Sent to CCL by: "Tomasz Grabarkiewicz" [grabar]*[man.poznan.pl] > This is a multi-part message in MIME format. > > ------=_NextPart_000_0037_01C5F1E5.AEF42D90 > Content-Type: text/plain; > charset="iso-8859-2" > Content-Transfer-Encoding: quoted-printable > > Hi CCLers, > Does anyone of you have any experience in dealing with a continuum = > solvation models of salt solutions? I'm interested in how the salt = > concentration affects the dynamics of a certain process. I'd like to = > perform a series of calculations in different concentrations. > Unfortunately I have no idea what value of the dielectric constant = > should be assigned in each case. > I searched through the internet but didn't find anything appropriate = > besides this (Hasted, J. B., Ritson, D. M. and Collie, C. H. (1948). = > "Dielectric Properties of Aqueous Ionic Solutions. Parts I and II," The = > Journal of Chemical Physics, vol 16, No.1. - but have no access to it) > > Can anyone help me? > Thanks, > Tomasz > ------=_NextPart_000_0037_01C5F1E5.AEF42D90 > Content-Type: text/html; > charset="iso-8859-2" > Content-Transfer-Encoding: quoted-printable > > > > charset=3Diso-8859-2"> > > > > >

Hi CCLers,

Does anyone of you have any experience in dealing with a continuum=20 > solvation models of salt solutions? I'm interested in how the salt = > concentration=20 > affects the dynamics of a certain process. I'd like to perform a series = > of=20 > calculations in different concentrations.

Unfortunately I have no idea what value of the dielectric = > constant=20 > should be assigned in each case.

I searched through the internet but didn't find anything = > appropriate=20 > besides this (Hasted, J. B., Ritson, D. M. and Collie, C. H. (1948). = > "Dielectric=20 > Properties of Aqueous Ionic Solutions. Parts I and II," The Journal = > of=20 > Chemical Physics, vol 16, No.1. - but have no access to it)

Can anyone help me?

Thanks,

Tomasz

> > ------=_NextPart_000_0037_01C5F1E5.AEF42D90--> > > From owner-chemistry@ccl.net Fri Nov 25 15:35:00 2005 From: "Igor Filippov Contr igorf{:}helix.nih.gov" To: CCL Subject: CCL: STRUCTURES TO SMILES Message-Id: <-30070-051125124644-26675-BiL21x1fDol12XcdN5tYxQ() server.ccl.net> X-Original-From: "Igor Filippov [Contr]" Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 25 Nov 2005 11:47:14 -0500 Mime-Version: 1.0 Sent to CCL by: "Igor Filippov [Contr]" [igorf-x-helix.nih.gov] No offense but questions like that make me wonder if people have stopped even trying to do something themselves, instead preferring just to dump it on the maillist in hopes somebody will do the job for them. Have you tried using Google ? It's quite a powerful tool for finding things. As for the answer to the question CACTVS, Pipeline Pilot, Daylight Toolkit all provide this functionality. In fact it's hard to find a chemoinformatics toolkit that DOESN'T do conversions to/from SMILES. If you just want something that converts a drawn structure into SMILES Java Molecular Editor as well as a dozen other applications will do the trick. If you only want to convert one or two structures you're welcome to use online tools at http://cactus.nci.nih.gov (e.g. - Online SMILES Translator). Igor On Fri, 2005-11-25 at 11:00, ragubalaji n ragubalaji_._gmail.com wrote: > Sent to CCL by: "ragubalaji n" [ragubalaji::gmail.com] > Hi all, > > I am looking for tool where SMILES strings can be generated from structures or connectivity tables. Could anybody tell me where I can find it? > Thank you very much. > > ragu > Bangalore > ragubalaji[#]gmail.com> From owner-chemistry@ccl.net Fri Nov 25 19:04:00 2005 From: "Aron Rogier Vandeputte wachtebeekse**hotmail.com" To: CCL Subject: CCL:G: Reproducing the Gaussian reported frequencies Message-Id: <-30071-051125113930-17585-FTtaKQ2a6xfrUo7w0B13iA ~ server.ccl.net> X-Original-From: "Aron Rogier Vandeputte" Sent to CCL by: "Aron Rogier Vandeputte" [wachtebeekse%x%hotmail.com] To obtain SCT-factors for a specific reaction, I need the frequencies and eigenvectors at different points along the reaction path. To do this, I performed an IRC calculation with the calcall option. In this way I got the second derivative matrix at every point. I wrote the matrix (after I made it symmetric) to Maple where I diagonalized it. The eigenvalues correspond to those reported by Gaussian, but when I try to convert them to frequencies something goes wrong. Gaussian output: ---------------- All quantities printed in internal units (Hartrees-Bohrs-Radians) The second derivative matrix: cc2 hc3 hcc3 hc4 hcc4 cc2 0.05230 hc3 -0.00001 0.34915 hcc3 -0.00775 -0.00970 0.11675 hc4 -0.00001 0.00088 -0.00807 0.34923 hcc4 -0.00775 -0.00807 0.02445 -0.00967 0.11679 dih4 0.00000 0.00000 0.00000 -0.01504 0.04380 hc5 -0.00001 0.00088 -0.00807 0.00089 -0.00807 hcc5 -0.00775 -0.00313 0.06337 -0.00313 0.06332 .... Maple worksheet: ---------------- hartree:=4.35975E-18; Joule/Hartree bohr:=0.52917725E-10: meter/bohr amu:=1.660538E-27: kg/amu hbar:=1.0545E-34: for j from 1 to 21 do if (Re(v[j])>0) then v[j] = j_th eigenvalue FREQUENCY[j]:=evalf(Re(1/2/Pi*sqrt(v[j]*hartree/bohr**2/amu)/100/3E8)); fi; od: The strange thing is that there is no correlation between the frequencies that I found and those produced by Gaussian. So, the fault can't be only caused by wrong conversions. I wonder what I'm doing wrong: isn't this the correct matrix for frequency calculation and how can I get the right one? Thanks in advance, Aron wachtebeekse%%hotmail.com From owner-chemistry@ccl.net Fri Nov 25 19:39:00 2005 From: "M. Nicklaus mn1-.-helix.nih.gov" To: CCL Subject: CCL: STRUCTURES TO SMILES Message-Id: <-30072-051125152947-29415-le2lsXUNv0hiz4DwEQKuSQ^server.ccl.net> X-Original-From: "M. Nicklaus" Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 25 Nov 2005 14:29:15 -0500 MIME-Version: 1.0 Sent to CCL by: "M. Nicklaus" [mn1!^!helix.nih.gov] Check out: http://cactus.nci.nih.gov/services/translate/ Marc Nicklaus On Fri, 25 Nov 2005, ragubalaji n ragubalaji_._gmail.com wrote: > Sent to CCL by: "ragubalaji n" [ragubalaji::gmail.com] > Hi all, > > I am looking for tool where SMILES strings can be generated from structures or connectivity tables. Could anybody tell me where I can find it? > Thank you very much. > > ragu > Bangalore > ragubalaji[#]gmail.com> > From owner-chemistry@ccl.net Fri Nov 25 20:14:00 2005 From: "errol lewars elewars%%trentu.ca" To: CCL Subject: CCL:G: TD method Message-Id: <-30073-051125105837-2646-7h+0ITqyyx1mi5cFVsm06A__server.ccl.net> X-Original-From: errol lewars Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii; format=flowed Date: Fri, 25 Nov 2005 10:55:11 -0500 MIME-Version: 1.0 Sent to CCL by: errol lewars [elewars|,|trentu.ca] 2005 Nov 25 hello, I am not sure what the problem is. I suggest you contact help in Contact Us at the Gaussian website. Note that excited state energies are ofter calculated with CIS. Good luck. E .Lewars ==== yang zhen na yangzn553===nenu.edu.cn wrote: >Sent to CCL by: "yang zhen na" [yangzn553:_:nenu.edu.cn] >Dear sir: > First, thanks for your help very much! second, I have another question to ask you. It is about Gaussian03. I want to get single point energy of the molecule in the excited state using TD method, I think I should use the keyword density=current, because this keyword causes the population analysis to use the current density rather than its default of the Hartree-Fock density. But when I use this keyword the computation will link died! I don't know how I handle with the problem. > yang> > > > > From owner-chemistry@ccl.net Fri Nov 25 20:49:00 2005 From: "moacyr .. iqsc.usp.br" To: CCL Subject: CCL: numerical atomic DFT program Message-Id: <-30074-051125184734-10758-3u75LiEG5MHT0i7ESU46DA- -server.ccl.net> X-Original-From: moacyr,iqsc.usp.br Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Fri, 25 Nov 2005 20:47:30 -0200 (BRST) MIME-Version: 1.0 Sent to CCL by: moacyr+/-iqsc.usp.br Hello Fellows! Does anyone know where I can get a relativistic '4-components' numerical DFT program for atoms? Thanks!! ----------------------------------------- WEBMail IQSC. http://www.iqsc.usp.br/