Alas, I think the poor submitter found out that = there's more than one way to split an SD file.=A0

OpenBabel has been = suggested for problem. There are several problems with that = proposal:

...

OK, enough = criticism, here is constructive = help:

No, no. Thanks very much! = We appreciate any and all bug reports and feedback -- as I mentioned in = my previous message to the list, no one had yet requested to use Open = Babel to split files into chunks of X molecules (where X > 1). That's = pretty easy for us to add (or anyone, since the code is = open.)

And we = obviously didn't know about those particular snags with SD files -- = certainly testing and testing and testing is the best approach. It's = important to hold chemistry software to a high standard.

So thanks to you, I filed = your helpful suggestions and bug reports into our public tracker. Please = feel free to keep the critiques coming:

http://sourceforge.net/= projects/openbabel

Cheers!

-Geoff

-Dr. Geoffrey Hutchison=A0 =A0 =A0 =A0 <grh25|cornell.edu>

Cornell University, Department of Chemistry and Chemical = Biology

Abru=F1a Group=A0 =A0 =A0 =A0 =A0 =A0 =A0 =A0 http://abruna.chem.cornell.edu= /

<= /HTML>= --Apple-Mail-8-671393312-- From owner-chemistry@ccl.net Tue Mar 20 12:07:01 2007 From: "Andrew Good Andrew.Good+*+bms.com" To: CCL Subject: CCL: CCG Excellence Student Travel Award Stipends Message-Id: <-33851-070320110923-19286-eFNcstYRmfpuOYgahVEmUA|,|server.ccl.net> X-Original-From: Andrew Good Content-return: prohibited Content-transfer-encoding: 7BIT Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Tue, 20 Mar 2007 10:08:42 -0400 MIME-version: 1.0 Sent to CCL by: Andrew Good [Andrew.Good a bms.com] 5 $1150 CCG Excellence Student Travel Award Stipends Available for the Fall 2007 Boston ACS The CCG Excellence Awards have been created to stimulate graduate student participation in COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are graduate students of the Americas in good standing who present work within the COMP program, either in oral or poster format. Winners receive $1,150, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the COMP Division Poster Session. For details of application requirments visit the CCG Award url at http://membership.acs.org/C/COMP/CCG/ccg.html From owner-chemistry@ccl.net Tue Mar 20 12:36:01 2007 From: "Aniko Simon aniko,,simbiosys.ca" To: CCL Subject: CCL: comparing database results Message-Id: <-33852-070320111334-21166-OBtMms360IT1noGRDqvxNw#,#server.ccl.net> X-Original-From: "Aniko Simon" Date: Tue, 20 Mar 2007 11:13:31 -0400 Sent to CCL by: "Aniko Simon" [aniko-.-simbiosys.ca] Hi Iain, eHiTS LASSO (free for academic users) does exactly what you need, i.e. finds compounds that have similar activity as your existing hit-list. In fact, eHiTS LASSO is even better than a mere structural similarity search, because it focuses on the similarity of interaction points without requiring the same underlying structure, thus you have a better chance of finding novel scaffolds while preserving the important pharmaceutical activity. For more information on eHiTS LASSO, please visit: http://www.simbiosys.ca/ehits_lasso/ Regards, Aniko Iain MacDougall iain.macdougallstudentmail.newcastle.edu.au wrote: > Sent to CCL by: "Iain MacDougall" [iain.macdougall\a/studentmail.newcastle.edu.au] > I have two sets of compounds from in silico database searching. I have compared the compounds and have found that none are identical, however I wish to find similar hits as well. I can do this by eye for small numbers of hits but this will be impossible for some of my larger hitlists. Does anyone know of freeware that will do some kind of structural comparison/similarity searching for me? > Thanks for your help!> From owner-chemistry@ccl.net Tue Mar 20 13:08:00 2007 From: "Ahmed El-Nahas amelnahas**hotmail.com" To: CCL Subject: CCL: Disk space and QCISD calculations Message-Id: <-33853-070320114255-10203-CQ7UEtZG1OI/CpHrwIuVfw]~[server.ccl.net> X-Original-From: "Ahmed El-Nahas" Date: Tue, 20 Mar 2007 11:42:51 -0400 Sent to CCL by: "Ahmed El-Nahas" [amelnahas() hotmail.com] A job running at QCISD needs about 50 GB of disk space and I have only about 30GB. I wonder if you know how to get it finished through forcing it to calculate two electron integrals when needed, which takes sometimes but will be no harm with limited disk space. I tried QCISD(direct) but it work as it can not see the direct option. Maxdisk option is not helpful in this respect, and may be some of the IOPs can help but I am not sure which one?. Regards Ahmed El-Nahas amelnahas,hotmail.com From owner-chemistry@ccl.net Tue Mar 20 13:46:01 2007 From: "Cross, Simon scross*tripos.com" To: CCL Subject: CCL: Babel problem (?) Message-Id: <-33854-070320122919-6361-w4Ll1e70p6VeVU7r82WtUg===server.ccl.net> X-Original-From: "Cross, Simon" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 20 Mar 2007 11:29:00 -0500 MIME-Version: 1.0 Sent to CCL by: "Cross, Simon" [scross,+,tripos.com] Hi Martin, SYBYL uses the file $TA_ROOT/tables/SybylAtomMaps to assign atom types using SLN definitions. So you could just add a rule in here to assign phosphate oxygens to your desired O.co2. This should work for dbtranslate command-line (via your script) and also SYBYL itself via the spreadsheet. Simon -----Original Message----- > From: owner-chemistry]=[ccl.net [mailto:owner-chemistry]=[ccl.net] Sent: Monday, March 19, 2007 3:31 PM To: Cross, Simon Subject: CCL: Babel problem (?) Sent to CCL by: Martin Lindh [martinlindh^_^yahoo.se] Thank you for your reply. When I have tried to import the sdf files directly into Sybyl. I get different atom types than if i first convert the files to mol2 format using Babel. For example I get the 03 type on charged oxygens in phosphate groups instead of 0co2. The Babel converted molecules (the one that convert well) seem to dock better in FlexX than if I convert them by importing them directly into Sybyl. I compute charges using the spl script dbcharges so I want to be able to import the molecules into Sybyl. regards Martin --- "Cross, Simon scross{=}tripos.com" skrev: > > Sent to CCL by: "Cross, Simon" [scross_-_tripos.com] > Martin, I'm not sure what the Babel problem is, but > a simple alternative > would be to import the SDF directly into the SYBYL > spreadsheet. Even > simpler would be to select SDF as the ligand input > file format from the > docking interface. > > If it is command-line translation you are after, > SYBYL's dbtranslate > utility should also be available to you. > > Regards, > > Simon > > ------------------------------------ > Dr Simon Cross > Product Manager > Tripos UK Ltd > scross(!)tripos.com > Tel +44 1908 650021 > Mob +44 7980 572278 > Fax +44 1908 650001 > ------------------------------------ > SYBYL, UNITY, and other products are exclusive > property of Tripos & are > protected by trademarks, copyrights, & patents as > appropriate. > > The information in this e-mail is confidential and > may have associated > legal obligations. It is intended for the exclusive > attention of the > addressee stated above and should not be copied or > disclosed to any > other. If you have received this transmission in > error, please contact > the sender. > > > -----Original Message----- > > From: owner-chemistry(!)ccl.net > [mailto:owner-chemistry(!)ccl.net] > Sent: Friday, March 16, 2007 5:16 PM > To: Cross, Simon > Subject: CCL: Babel problem (?) > > > Sent to CCL by: "Martin Lindh" > [martinlindh-$-yahoo.se] > Hi > > I prepare ligands using LigPrep (Maestro). Since I > want to dock these > ligands > in FlexX (Sybyl), I export the ligands from Maestro > as a .sdf file. I > then > use Babel to convert the .sdf file to a multi .mol2 > file. The .mol2 file > is > then imported into Sybyl. > > During this process some(!) of the ligands get > strange mol2 formating. > > Part of a molecule that is translated correctly into > the mol2-file: > [A]ATOM > 1 P1 -7.7746 0.3497 0.1484 P.3 1 <1> > 0.1085 > 2 O1 -7.2207 1.7666 -0.1209 O.2 1 <1> > -0.4607 > 3 O2 -7.9571 -0.5515 -1.0931 O.co2 1 <1> > -0.3575 > > Part of a molecule that is NOT translated correctly > in mol2-file: > > 28 C 14.2736 6.1106 -1.8492 C.ar 0 > UNK0 0.1493 > 29 N 14.3973 5.3090 -0.7250 N.ar 0 > UNK0 -0.2079 > 30 N 13.7198 8.3248 -1.0353 N.pl3 0 > UNK0 -0.3413 > 31 C1* 15.1231 2.8403 -3.4280 C.3 1 > UNK1 0.1683 > 32 O4* 15.0326 3.1353 -4.7858 O.3 1 > UNK1 -0.3456 > 33 C4* 13.7316 2.8114 -5.2536 C.3 1 > UNK1 0.1126 > > Anyone seen this problem and have suggestions of > what to do? > > Thank you in advance > Martinhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt > > > -= 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 a > sign. You can also > look up the X-Original-From: line in the mail > header.> > E-mail to administrators: CHEMISTRY-REQUEST a 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/> > > > _________________________________________________________ Flyger tiden iväg? Fånga dagen med Yahoo! Mails inbyggda kalender. Dessutom 250 MB gratis, virusscanning och antispam. Få den på: http://se.mail.yahoo.comhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt From owner-chemistry@ccl.net Tue Mar 20 17:07:01 2007 From: "Curt M. Breneman brenec#rpi.edu" To: CCL Subject: CCL: ACS Boston - "Emerging Technologies in Computational Chemistry" competition symposium is now open for entries! Message-Id: <-33855-070320161404-10462-QWK3VOPT87CDVAjjVg7Yjg=server.ccl.net> X-Original-From: "Curt M. Breneman" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Tue, 20 Mar 2007 15:05:57 -0400 MIME-Version: 1.0 Sent to CCL by: "Curt M. Breneman" [brenec() rpi.edu] 2007 Competition Symposium on "Emerging Technologies in Computational Chemistry" $1,000 prize to be awarded at the ACS national meeting, Boston, MA. The Computers in Chemistry Division (COMP) of the ACS will hold the eighth annual Symposium on Emerging Technologies in Computational Chemistry at the American Chemical Society National Meeting, Boston, MA, August 19-23, 2007. The objective of the symposium is to stimulate, reward, and publicize major methodological advances in computational chemistry. The talks will be evaluated by a Panel of Experts on the quality of the presentation and the impact that the research will have on the future of computational chemistry and allied sciences. The symposium is ideal for presenting your latest and best research on new techniques, applications and software development. Schrodinger, Inc. sponsors the $1,000 award for the best talk at the symposium. All are invited to participate. To enter the competition, you should submit a regular short ACS abstract via http://oasys.acs.org/ prior to the OAsys deadline. It is also necessary to email a long (~1,000-word) abstract to the organizer. The presentations must be original, novel and concise. After receipt, the long abstracts will be evaluated by experts to determine which individuals will be selected to give oral presentations at the symposium. Finalists will be notified well in advance of the meeting. Presentations submitted through OAsys that cannot be part of the Emerging Technologies Symposium will be rescheduled in another appropriate COMP session at the Boston meeting. Inquiries and applications should sent to: Prof. Curt M. Breneman Director, RECCR Center for Cheminformatics Research Department of Chemistry Rensselaer Polytechnic Institute Troy, NY 12180 E-mail: brenec_at_rpi.edu From owner-chemistry@ccl.net Tue Mar 20 18:00:01 2007 From: "Alessandro Casoni alessandro.casoni a unimi.it" To: CCL Subject: CCL: Protein Morpher Message-Id: <-33856-070320121647-31103-Tixf4Kam84fPqpXBXzr6kg=server.ccl.net> X-Original-From: "Alessandro Casoni" Date: Tue, 20 Mar 2007 12:16:42 -0400 Sent to CCL by: "Alessandro Casoni" [alessandro.casoni!A!unimi.it] Hi, does anyone know any software (preferably open source) able to do protein morphing? I have a receptor in 2 conformations and I want to build an intermediate conformation. Any help will be appreciated... Alessandro From owner-chemistry@ccl.net Tue Mar 20 19:46:01 2007 From: "Warren DeLano warren * delsci.com" To: CCL Subject: CCL: Protein Morpher Message-Id: <-33857-070320193445-14283-6Wpnn7KDp2rpt6LSU0DJ8A^^server.ccl.net> X-Original-From: "Warren DeLano" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Date: Tue, 20 Mar 2007 15:43:15 -0800 MIME-Version: 1.0 Sent to CCL by: "Warren DeLano" [warren[A]delsci.com] Allessandro, It's not open source nor free, but one of the benefits I provide paid-up PyMOL sponsors is a clumsy little command-line extension that actually does this quite well, even with large conformational changes. Free alternatives include include lsqman and the Yale Morph Server. Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice: 1-650-283-6945 Fax: 1-650-989-4082 US Mail: PO Box 1118, Palo Alto, CA 94302-1118, USA > -----Original Message----- > From: owner-chemistry__ccl.net [mailto:owner-chemistry__ccl.net] > Sent: Tuesday, March 20, 2007 3:46 PM > To: Warren DeLano > Subject: CCL: Protein Morpher > > > Sent to CCL by: "Alessandro Casoni" > [alessandro.casoni!A!unimi.it] Hi, does anyone know any > software (preferably open source) able to do protein > morphing? I have a receptor in 2 conformations and I want to > build an intermediate conformation. > > Any help will be appreciated... > > Alessandro > > > > -= 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.> Conferences: > http://server.ccl.net/chemistry/announcements/conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, > Password: search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > -+-+-+-+-+ > > > > > > > > From owner-chemistry@ccl.net Tue Mar 20 22:21:01 2007 From: "Thomas Joseph alabarae_+_yahoo.com" To: CCL Subject: CCL: pharmacophore freeware Message-Id: <-33858-070320220251-19779-0jtokRp/jbtQJvYadJjo0Q[]server.ccl.net> X-Original-From: "Thomas Joseph" Date: Tue, 20 Mar 2007 22:02:47 -0400 Sent to CCL by: "Thomas Joseph" [alabarae(!)yahoo.com] is there any pharmacophore generation freeware available for academics From owner-chemistry@ccl.net Tue Mar 20 22:57:01 2007 From: "Arindam Ganguly arindamganguly__gmail.com" To: CCL Subject: CCL: Replica exchange molecular dynamics REMD Message-Id: <-33859-070320223212-25823-zaeHF4OFT+R4W6wWodnm+g[a]server.ccl.net> X-Original-From: "Arindam Ganguly" Date: Tue, 20 Mar 2007 22:32:08 -0400 Sent to CCL by: "Arindam Ganguly" [arindamganguly|gmail.com] Hi All Computational Chemist, i am trying to run a Replica exchange molecular dynamics calculation on a protein, i mean a 15peptide residue. i have access to both GROMACS(www.gromacs.org) and also VMD(http://www.ks.uiuc.edu/Research/vmd/). has anybody any REMD calculations using these packages. any help, i mean tutorial, any sample run information, is highly appreciated. thanks. Arindam Ganguly Graduate Student UMKC-Dept. of Chemistry