From owner-chemistry@ccl.net Thu Jul 2 02:09:01 2009 From: "Jerome Kieffer jerome.Kieffer|terre-adelie.org" To: CCL Subject: CCL: Conformation search help Message-Id: <-39683-090702020052-2322-dptICmaajcF4SbQRZJHVMA : server.ccl.net> X-Original-From: Jerome Kieffer Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-15 Date: Thu, 2 Jul 2009 08:00:38 +0200 Mime-Version: 1.0 Sent to CCL by: Jerome Kieffer [jerome.Kieffer::terre-adelie.org] On Wed, 1 Jul 2009 13:03:17 +0530 "Vikash kumar kvikash01()gmail.com" wrote: >=20 > Sent to CCL by: "Vikash kumar" [kvikash01|,|gmail.com] > Hi All >=20 > I want to know, is there any freely available Monte Carlo conformational > search for ligand like sucrose present on the web or not. >=20 did you gave a look on Ghemical ? --=20 J=E9r=F4me KIEFFER =20 http://www.terre-adelie.org From owner-chemistry@ccl.net Thu Jul 2 03:26:00 2009 From: "Mikko Vainio mikko.vainio!A!abo.fi" To: CCL Subject: CCL: Conformation search help Message-Id: <-39684-090702023450-14583-H8zwSEHiorl8bVIFdA2/7Q],[server.ccl.net> X-Original-From: Mikko Vainio Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=UTF-8; format=flowed Date: Thu, 02 Jul 2009 09:02:41 +0300 MIME-Version: 1.0 Sent to CCL by: Mikko Vainio [mikko.vainio|-|abo.fi] Vikash kumar kvikash01()gmail.com wrote: > Sent to CCL by: "Vikash kumar" [kvikash01|,|gmail.com] > Hi All > > I want to know, is there any freely available Monte Carlo conformational > search for ligand like sucrose present on the web or not. > > Balloon is free and can handle flexible ring structures: http://users.abo.fi/mivainio/balloon/ It is based on a genetic algorithm, which is a stochastic method akin to Monte Carlo. Cheers, Mikko From owner-chemistry@ccl.net Thu Jul 2 15:36:00 2009 From: "Abel Jonckheer abel.jonckheer,fys.kuleuven.be" To: CCL Subject: CCL: Amber 2 OPLS Message-Id: <-39685-090702085310-21069-+Py7MxAF1EMDx/g+3f8dnQ[#]server.ccl.net> X-Original-From: Abel Jonckheer Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 02 Jul 2009 14:46:20 +0200 MIME-Version: 1.0 Sent to CCL by: Abel Jonckheer [abel.jonckheer!^!fys.kuleuven.be] Dear All, I would like to use amber99 charges calculated for a TRP excited state into an OPLS based MD simulation. Would it be sufficient to calculate the factor ex. state/grnd. state of the Amber charges and apply then to the OPLS ground state charges? Thank you for your help, Abel -- ------------------------------------------------ Abel Jonckheer KULeuven, Laboratory for Biomolecular Dynamics Celestijnenlaan 200G B-3001 Heverlee 016/327284 ------------------------------------------------ From owner-chemistry@ccl.net Thu Jul 2 16:11:00 2009 From: "Joseph Durant Joseph.Durant^symyx.com" To: CCL Subject: CCL: Pipeline pilot: chemical reaction .rxn Message-Id: <-39686-090701204745-16667-38JxFbzyuVIRSM2F80GYCQ[#]server.ccl.net> X-Original-From: Joseph Durant Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Wed, 01 Jul 2009 16:47:26 -0700 MIME-Version: 1.0 Sent to CCL by: Joseph Durant [Joseph.Durant*symyx.com] The 1's and 0's in the bond lines are reaction center marks... 0 = unmarked 1 = a center 2 = unchanged 4 = made/broken 8 = bond order changes Additionally, the last 3 can be added together, so 6 = 2 + 4 = unchanged or made/broken (used for example when there are two products). Your renderer is rendering "a center" with an asterisk. Alessio Moriconi alessio.moriconi * dompe.it wrote: > Sent to CCL by: "Alessio Moriconi" [alessio.moriconi-$-dompe.it] > Hi all, > I was wondering if any one would be able to help me. > I have a problem with an .rxn file containing a list of multiple and different reactions, in the form: > > A -> B > > I am using Pipeline Pilot 7.5 to manipulate this file. > When I view the .rxn with an HTML molecular visualizer, for each reaction, some asterisks appear in several bonds (the reacting centers), generating a substructure. In the corresponding rxn file, these bonds (those highlighted by the asterisk) are flagged by 1, the others by 0 (last column), like: > > $MOL > > -ISIS- 02010817122D > > 5 4 0 0 0 0 0 0 0 0999 V2000 > 3.4182 -3.4103 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0 > 2.7013 -2.1664 0.0000 O 0 0 0 0 0 0 0 0 0 3 0 0 > 3.4182 -2.5809 0.0000 C 0 0 3 0 0 0 0 0 0 4 0 0 > 1.9890 -2.5809 0.0000 C 0 0 0 0 0 0 0 0 0 6 0 0 > 4.1372 -2.1741 0.0000 O 0 0 0 0 0 0 0 0 0 8 0 0 > 5 3 1 0 0 0 1 > 2 4 1 0 0 0 0 > 2 3 1 0 0 0 1 > 3 1 1 0 0 0 0 > M END > > > I would like to write (canonical smiles) in a different file only these substructures in such a way for each reaction of the .rxn file. > Thanks for any help. > > Alessio> > -- Joe Durant Joseph.Durant ~ symyx.com Symyx Technologies, Inc. 2440 Camino Ramon, Suite 300, San Ramon, CA 94583 voice: (925) 543-7511 -------------- "Until the twentieth century, reality was everything that humans could see, hear, touch, smell, or taste. 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