From owner-chemistry@ccl.net Tue Mar 17 04:28:01 2009 From: "Martin Bohl martin : moldiscovery.com" To: CCL Subject: CCL: Release of MoKa 1.1 software Message-Id: <-38871-090317042515-18948-TlvjoS31L143hi97Y8/JiA^-^server.ccl.net> X-Original-From: "Martin Bohl" Date: Tue, 17 Mar 2009 04:25:11 -0400 Sent to CCL by: "Martin Bohl" [martin- -moldiscovery.com] Dear Colleagues, We are proud to announce the immediate availability of the next major release of our pKa modelling software, MoKa 1.1, featuring: * New and improved pKa prediction models * Improved tautomers enumeration code, with abundance estimation * LogP and LogD calculation including: - LogD calculation with user defined LogP values - LogP calculation with user defined LogD value * Improved 2D structure layout * Interactive 2D structure editing * Rename structures by SD attribute * Improved mol2 parsing Improved robustness, ease of use, and integration with Accelrys' Pipeline Pilot complete the feature set. For further details about availability of MoKa and the Pipeline Pilot integration components, see: http://www.moldiscovery.com/soft_moka.php http://www.moldiscovery.com/integration.php For pricing information, please contact our sales department: sales_at_moldiscovery.com Kind regards, Martin Dr. Martin Bohl Commercial Director Molecular Discovery Ltd From owner-chemistry@ccl.net Tue Mar 17 09:56:00 2009 From: "Christoph Steinbeck steinbeck===ebi.ac.uk" To: CCL Subject: CCL: 2nd Call for registration: CDK workshop in Hinxton, Cambridge, on April 20/21, 2009 Message-Id: <-38872-090317083109-27992-+2qddkiM/kaSHNq/67bhLQ=server.ccl.net> X-Original-From: Christoph Steinbeck Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Tue, 17 Mar 2009 11:32:15 +0000 MIME-Version: 1.0 Sent to CCL by: Christoph Steinbeck [steinbeck(_)ebi.ac.uk] The Chemistry Development Kit (CDK) team is glad to announce the Spring 2009 CDK workshop [1] held at the European Bioinformatics Institute (EBI). More than two years have passed since the last CDK workshop in Cologne and we hope to have these great events more regularly again. So far, 23 participants from Industry and Academia are registered and we are sure it will be a lively and inspiring event again. We have a capacity of 40, so there are still some places left. We are glad that the EBI Industry Program as well as the EBI outreach and training department are sponsoring the event. This means that things will be much more organized as they used to be :-) . We are going to have one day (lunch time to lunch time the next day) of tutorials on how to use CDK and talks on research using the CDK. Afterwards, we'll have our usual free-form developers workshop for the rest of the second day with all the usual fun (bug squashing and whatever you like). Both the evening of the 20th and the 21st will be opportunities for enjoying refreshments. We also have a small nominal registration fee of 50 Pounds to cover the costs for the workshop dinner and other food and drinks. Cheers, Chris [1] http://www.ebi.ac.uk/training/handson/course_090420_cdk_industry.html [2] https://apps.sourceforge.net/mediawiki/cdk/index.php?title=Spring2007Workshop -- Dr. Christoph Steinbeck Head of Chemoinformatics and Metabolism European Bioinformatics Institute (EBI) Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD UK Phone +44 1223 49 2640 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From owner-chemistry@ccl.net Tue Mar 17 10:30:00 2009 From: "Manchester, John John.Manchester%astrazeneca.com" To: CCL Subject: CCL: QSAR software Message-Id: <-38873-090317094428-472-AIUdNvfTpuj4Z1ZVYv+mZA|-|server.ccl.net> X-Original-From: "Manchester, John" Content-class: urn:content-classes:message Content-Transfer-Encoding: base64 Content-Type: text/plain; charset="UTF-8" Date: Tue, 17 Mar 2009 08:43:54 -0400 MIME-Version: 1.0 Sent to CCL by: "Manchester, John" [John.Manchester---astrazeneca.com] U29ycnkgYWJvdXQgdGhhdCBsYXN0IHBvc3QuICBJJ20gdG9sZCB0aGF0IHNvcnQgb2YgZ2FyYmxp bmcgY291bGQgYmUgZHVlIHRvIGVkZGllcyBpbiB0aGUgc3BhY2UtdGltZSBjb250aW51dW0sIGJ1 dCB0aGF0IG9uZSBzaG91bGRuJ3QgcGFuaWMuDQoNCkknbGwgdHJ5IGFnYWluLiAgV2UgaGF2ZSBz b21lIGNvZGUgdGhhdCBnZW5lcmF0ZXMgM0QgUVNBUiBkZXNjcmlwdG9ycywgd2hpY2ggY2FuIGJl IGRvd25sb2FkZWQgZnJvbSBodHRwOi8vcHVicy5hY3Mub3JnL2RvaS9zdXBwbC8xMC4xMDIxL2Np ODAwMDA5dS4gIEl0IHVzZXMgdGhlIE9FY2hlbSBsaWJyYXJ5LCB3aGljaCBJJ20gYWxzbyB0b2xk IGNhbiBiZSBvYnRhaW5lZCBmcmVlIGZvciBhY2FkZW1pYyB1c2UgZnJvbSBPcGVuRXllIChodHRw Oi8vd3d3LmV5ZW9wZW4uY29tKS4NCg0KVGhlIGNvZGUgZG9lc24ndCBkbyBtb2xlY3VsYXIgYWxp Z25tZW50IChPcGVuZUV5ZSdzIFJPQ1MgbWlnaHQgY29tZSBpbiBoYW5keSBmb3IgdGhhdCkuICBX ZSd2ZSBoYWQgZ29vZCBsdWNrIHdpdGggUiBmb3IgbW9kZWwgZml0dGluZyAoaHR0cDovL3d3dy5y LXByb2plY3Qub3JnLykuDQoNCkdvb2QgbHVjaywNCkpvaG4NCg0KDQotLS0tLU9yaWdpbmFsIE1l c3NhZ2UtLS0tLQ0KRnJvbTogb3duZXItY2hlbWlzdHJ5K2pvaG4ubWFuY2hlc3Rlcj09YXN0cmF6 ZW5lY2EuY29tQGNjbC5uZXQNClttYWlsdG86b3duZXItY2hlbWlzdHJ5K2pvaG4ubWFuY2hlc3Rl cj09YXN0cmF6ZW5lY2EuY29tQGNjbC5uZXRdT24NCkJlaGFsZiBPZiBNYW5jaGVzdGVyLCBKb2hu IEpvaG4uTWFuY2hlc3RlcipfKmFzdHJhemVuZWNhLmNvbQ0KU2VudDogRnJpZGF5LCBNYXJjaCAx MywgMjAwOSA1OjI0IFBNDQpUbzogTWFuY2hlc3RlciwgSm9obg0KU3ViamVjdDogQ0NMOiBRU0FS IHNvZnR3YXJlDQoNCg0KSe22gC1qdyF6XiEhxqdyF9qycShNBTUZBNCBzZXVsMiB1IHMgM29yY0Q RU0FSE3Jjd25yb3JlOiBoei8vdWJzLnMucmcxL3UuCXQgc2VwrQ9FcmF5LCB3aHRhciBzZTJvT0V 5ZSA6Ly93Lnllb00KDQpZdSB3aXRpc29zb3dhcmUyIHRpcy4SMK00IHVsdCB0bzJuNGhyZTJlOSB tdWxwrTZhdWNwrTJhcmV0Lg0KDQpKTQoNCg9yaU1zYU0KRnJveiBvd25yLXkranRlcmF6ZW5ATQp bdG83bnIteStqdGVyYXplbkBdT00KQk9OcK0KQ0KyaXRlc2V1Lk0KU0ZyaXksIE1yY3MsNCBQTQ0 KVE10ZXIsCk0KU3ViQ0KDQowRU0FSM293YXJlDQoNCg0KDQpTdCB0bwNCg0KMOiAiTnCtCkNCsml 0ZXNlW11eW3UuXQ0KRHIgU3JnTQoNCkkyZTUgd2l0bzIgdCBzb3JjcmV3YXJlDQpyb3JhcK0yIHR odWx0aXZhcmlwrTVsciBzY3JpdG9wrQ0Kc290aXNlcmN0aHdlVHNjcml0b3CtMK0NCnRocm91IHd pc2g0bzZldGl0ZQl0IHkgYnRhdCB0bw0KdGhybHkgbHJndGlzY3JpdG9wrTJvdml0aHCtM2NyaXR vTQp1bHRvciBHVUkyb3RoQ0KESzRvdCkNCg0Kei8vcmd1aHQvdmEzYzRtTQoNClR0aHQgeSBrd2x 0aHJlMK0zb3JjQ0KPTUZBM293YXJlDQp0IHRocmUNCg0KQXRlciB0aHVsdGlzY3JpdG9zLANCtGx zb00KcmVyZXNpc293YXJlNG80YXNoMmV0aXNod2V0aHVsdGVNCnNjcml0b3CtNGh0aXZpcm95IG9 0ZXJldC4TTHCtMmVNCnRscmV0IHZpcm90IHIgd29ya3dpdGgNCnVsdGl2YXJpdGUyb3MgNGhyIHR ocykDQrQgdGh0b3CtDQp3ZUNCtGxQTFMQQ0KSMmVyZXNpQU5ON2h0bk0KDQp6Ly93LnNjcmcyaV9 yaXdudGVNT0RFTElORwFORANCj05UUk9MFE9PTFMNCg0KQnQsDQpOcyANCg0KDQoNChNyZ01yZXM tU00Kc2VyZ3Jlcy1zYXRncmF0ZXIudWsNCjduci15I2NzLzMvMSBQTQ0KDQpTdCB0bwNCg0KME3J nTXJlcy1TTQpbc2VyZ3Jlcy1zYV5fXnRncmF0ZXIudWtdDQpEciBBTQoNCkkyIFFTQVIzb3dhcmU 0aHIgdGh0aHQgdWxyIHJldGxNCnZhVHJpcy4JN291bHZleSBncmF0ZXVsM29wrTRvDQpyb3Zpd2l 0aDNvdGlzLgk0aXVscmx5IGl0ZXJldGVyZU0Kc29yY3Nvd2FyZQ0KDQpUdSB2ZXkgbXVjdmFNCg0 KU3JnTXJlcy1TTQpUVXZlc2l5IG9NdGVNCk10ZU0KVXRlS3ovL3cudC9zZV9fc2F6Ly93LnQvdWJ fdW51YjNodG16Ly93LnQvcy5NCg0KDQoUcK0wrTRvdGl5IGF0bzNhdGhzY3JpdCANClRyZXZlciB 0aHJlcK00aHRociB0aHNhc2UNCnRocmFyYXRlcK00aHRvdG80aHNpWXUgc28NCnRoWA9yaUZyb3o gbHRoci4NCg0KRTRvNWJzY3JpQ0KIRU1JU1RSWUB0IHIgc2UNCjovL3cudC9Z2ktYmluL2NjbC9z ZW5kX2NjbF9tZXNzYWdlDQoNCkUtbWFpbCB0byBhZG1pbmlzdHJhdG9yczogQ0hFTUlTVFJZLVJF UVVFU1RAY2NsLm5ldCBvciB1c2UNCiAgICAgIGh0dHA6Ly93d3cuY2NsLm5ldC9jZ2ktYmluL2Nj bC9zZW5kX2NjbF9tZXNzYWdlDQoNClN1YnNjcmliZS9VbnN1YnNjcmliZTogDQogICAgICBodHRw Oi8vd3d3LmNjbC5uZXQvY2hlbWlzdHJ5L3N1Yl91bnN1Yi5zaHRtbA0KDQpCZWZvcmUgcG9zdGlu ZywgY2hlY2sgd2FpdCB0aW1lIGF0OiBodHRwOi8vd3d3LmNjbC5uZXQNCg0KSm9iOiBodHRwOi8v d3d3LmNjbC5uZXQvam9icyANCkNvbmZlcmVuY2VzOiBodHRwOi8vc2VydmVyLmNjbC5uZXQvY2hl bWlzdHJ5L2Fubm91bmNlbWVudHMvY29uZmVyZW5jZXMvDQoNClNlYXJjaCBNZXNzYWdlczogaHR0 cDovL3d3dy5jY2wubmV0L2NoZW1pc3RyeS9zZWFyY2hjY2wvaW5kZXguc2h0bWwNCg0KSWYgeW91 ciBtYWlsIGJvdW5jZXMgZnJvbSBDQ0wgd2l0aCA1LjcuMSBlcnJvciwgY2hlY2s6DQogICAgICBo dHRwOi8vd3d3LmNjbC5uZXQvc3BhbW1lcnMudHh0DQoNClJURkk6IGh0dHA6Ly93d3cuY2NsLm5l dC9jaGVtaXN0cnkvYWJvdXRjY2wvaW5zdHJ1Y3Rpb25zLw0KDQoNCgFqaml2aXpqAXl6eXZ6amp6 enFcemkSEE1ycnVqCCFhUHF6cXpKcntyesOWBXJybnp6csuecXJ6cUlyenJ6cnUhcsOWRXLLonIN Cg== From owner-chemistry@ccl.net Tue Mar 17 12:32:02 2009 From: "nathanel weill naweill:_:gmail.com" To: CCL Subject: CCL: PASS source Message-Id: <-38874-090317123114-21242-mj8JHQVcTn/Wa/0d9T2G6A+/-server.ccl.net> X-Original-From: "nathanel weill" Date: Tue, 17 Mar 2009 12:31:10 -0400 Sent to CCL by: "nathanel weill" [naweill**gmail.com] Dear CCLers, I would like to use PASS program for cavity detection. On the publication, it is mentionned that the source code should be freely avilable on ccl software repository. Unfortunately, I did nit find it... Is someone still have the source code? Thanks Nathanael Weill From owner-chemistry@ccl.net Tue Mar 17 16:01:00 2009 From: "Sergio Mares-Samano sergio.mares-samano,postgrad.manchester.ac.uk" To: CCL Subject: CCL: Protonation states Message-Id: <-38875-090317155815-1486-/JcyxNyDOyNqXf9Ij34SvQ-.-server.ccl.net> X-Original-From: Sergio Mares-Samano Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Tue, 17 Mar 2009 19:57:53 +0000 MIME-Version: 1.0 Sent to CCL by: Sergio Mares-Samano [sergio.mares-samano/a\postgrad.manchester.ac.uk] Hi, Which software (free/open source) can I use to assign the correct ligand protonation forms? I have a database of around 5000 molecules (smile format) and used open babel to convert them into the SDF's. After performing a google search, I found that OpenBabel was a good option to get the SDF's from the smiles. Now however, I'm struggling to find a program to assign the correct charges according to a certain pH e.g. 7. Any suggestions? Thank you very much in advance, Sergio Mares-Samano From owner-chemistry@ccl.net Tue Mar 17 17:40:00 2009 From: "anu B anubamgbelu||yahoo.com" To: CCL Subject: CCL: Excited states calculations Message-Id: <-38876-090317152556-30554-U5wW8XM+kg1oyiI5FXOQwg|-|server.ccl.net> X-Original-From: "anu B" Date: Tue, 17 Mar 2009 15:25:52 -0400 Sent to CCL by: "anu B" [anubamgbelu|yahoo.com] Hi All, I am performing Time dependent-DFT calculations on some organic molecules. I did the initial geometric optimization and included the keyword "scf=nosymm,qc,NoVarAcc" in the route section, because the job crashed at first with an error message.(SCF is confused). Now i am running the TDDFT calculations using the initial optimized geometry. However, the job crashed and the error message was the smallest alpha delta epsilon is -0.15430889D-04.. I did not include the keyword "scf=nosymm,qc,NoVarAcc" in the TDDFT calculations. Any advice on this would be appreciated. thanks anu. From owner-chemistry@ccl.net Tue Mar 17 18:33:00 2009 From: "Wayne Steinmetz WES04747]|[pomona.edu" To: CCL Subject: CCL: Protonation states Message-Id: <-38877-090317173815-4738-go1tk2t1lfK9lfOTqUzaKw_._server.ccl.net> X-Original-From: "Wayne Steinmetz" Content-class: urn:content-classes:message Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="US-ASCII" Date: Tue, 17 Mar 2009 14:38:00 -0700 MIME-Version: 1.0 Sent to CCL by: "Wayne Steinmetz" [WES04747!=!pomona.edu] I make extensive use of molecular mechanics with the Merck Molecular Force Field. Both SYBYL (expensive) and Spartan (fairly cheap) employ it. The process is fairly simple: 1) Draw the structure. The atoms types will be implied by the structure. 2) Provide the total charge on the species in Spartan. The force field engine will do the rest. I just verified this with a test calculation on the ammonium ion with Spartan. Now there is a catch. You have to know the predominant molecular species at pH 7. That is a chemical question requiring knowledge or an estimate of the pKa. You may want to do a calculation for both the acid and the conjugate base. -----Original Message----- > From: owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu,ccl.net [mailto:owner-chemistry+wsteinmetz=3D=3Dpomona.claremont.edu,ccl.net] On Behalf Of Sergio Mares-Samano sergio.mares-samano,postgrad.manchester.ac.uk Sent: Tuesday, March 17, 2009 12:58 PM To: Wayne Steinmetz Subject: CCL: Protonation states Sent to CCL by: Sergio Mares-Samano [sergio.mares-samano/a\postgrad.manchester.ac.uk] Hi, Which software (free/open source) can I use to assign the correct ligand protonation forms? I have a database of around 5000 molecules (smile=20 format) and used open babel to convert them into the SDF's. After=20 performing a google search, I found that OpenBabel was a good option to=20 get the SDF's from the smiles. Now however, I'm struggling to find a=20 program to assign the correct charges according to a certain pH e.g. 7. Any suggestions? Thank you very much in advance, Sergio Mares-Samano -=3D This is automatically added to each message by the mailing script = =3D-http://www.ccl.net/cgi-bin/ccl/send_ccl_messageSubscribe/Unsubscribe:=20Job: http://www.ccl.net/jobs=20http://www.ccl.net/spammers.txt------------------------------------------------------------- This message has been scanned by Postini anti-virus software. =0D