From owner-chemistry@ccl.net Tue Feb 9 10:52:00 2010 From: "Jimmy Stewart MrMOPAC++openmopac.net" To: CCL Subject: CCL: MOPAC2009 keyword PM6-DH2 now active Message-Id: <-41222-100209104731-26779-lE52QOoe25jGYsmWvCtSBQ[a]server.ccl.net> X-Original-From: Jimmy Stewart Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1"; format=flowed Date: Tue, 09 Feb 2010 08:41:32 -0700 Mime-Version: 1.0 Sent to CCL by: Jimmy Stewart [MrMOPAC]~[openmopac.net] Now that the non-covalent interaction correction=20 developed by Pitonak, et.al., has been published,=20 see: Korth M, Piton=E1k M, Rez=E1c J, Hobza P "A=20 Transferable H-Bonding Correction for=20 Semiempirical Quantum-Chemical Methods" J Chem=20 Theory and Computation 6:344-352 (2010), the=20 authors have approved the addition of the keyword=20 PM6-DH2 to MOPAC2009. As a result, the keyword=20 PM6-DH2 is now active in MOPAC2009, Version 10.040 for Windows, Mac, and= Linux. For more information, please see: Abstract: http://pubs.acs.org/doi/abs/10.1021/ct900541n Keyword: http://openmopac.net/manual/pm6_dh2.html Accuracy: http://openmopac.net/manual/pm6_dh2_accuracy.html Maintenance: http://openmopac.net/Maintenance.html ( -$- -$- ) = .-----------------oOOo----(_)----oOOo--------------------------------------= . | James J. P. Stewart | = | | Stewart Computational Chemistry | E-mail: MrMOPAC-$-OpenMOPAC.net = | | 15210 Paddington Circle | 39/03/15 N, 104/49/29 W = | | Colorado Springs CO 80921-2512 | http://openmopac.net/ = | | USA | SKYPE: Jimmy.Stewart2 GMT 1500 -= 0200| | .ooo0 | Phone: USA +(719) 488-9416 = | | ( ) Oooo.| = | .-----------------------\ (----( = )---------------------------------------. \_) ) / (_/ =20 From owner-chemistry@ccl.net Tue Feb 9 11:55:00 2010 From: "Xavier xdeupi[*]gmail.com" To: CCL Subject: CCL: software to list chi1 angles Message-Id: <-41223-100208055317-8813-S1sQQce0T8Zp8BRk/PXGFg(0)server.ccl.net> X-Original-From: Xavier Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=us-ascii Date: Mon, 8 Feb 2010 10:43:21 +0100 Mime-Version: 1.0 (Apple Message framework v1077) Sent to CCL by: Xavier [xdeupi+*+gmail.com] Hi Reynier, You can use Dang http://kinemage.biochem.duke.edu/software/dang.php Xavier Xavier Deupi Laboratory of Computational Medicine Biostatistics Unit. School of Medicine Universitat Autonoma de Barcelona Bellaterra, 08193 (Barcelona) Catalunya, EU lmc.uab.cat On Feb 6, 2010, at 7:40 PM, Reynier Suard az = reynier.suardiaz-x-gmail.com wrote: >=20 > Sent to CCL by: "Reynier Suard az" [reynier.suardiaz:+:gmail.com] > Dear all > I am looking for a free software that be able to list chi1 dihedral = angles values of proteins from a pdb file as input. > thanks in advance > reynier >=20 >=20 >=20 >=20 > -- > _______________________________________________________ >=20 > Dr. Reynier Suardaz e-mail: reynier(-)fq.uh.cu > Dpto.de Qumica Fsica telf.: +53 7 8780684 > Facultad de Qumica La Habana, 10400 > Universidad de La Habana Cuba > url: http://www.fq.uh.cu/investig/gqf/e/lrsdr_en.html > _______________________________________________________ >=20 >=20 >=20 From owner-chemistry@ccl.net Tue Feb 9 12:30:01 2010 From: "John john() ccdc.cam.ac.uk" To: CCL Subject: CCL: software to create a pharmacophore Message-Id: <-41224-100209081245-9357-m2yU3/7eGv3l7OzlN6mBDg---server.ccl.net> X-Original-From: "John" Content-Language: en-gb Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Tue, 9 Feb 2010 12:16:17 -0000 MIME-Version: 1.0 Sent to CCL by: "John" [john.:.ccdc.cam.ac.uk] Dear Alberto, Another possibility you might want to consider is to use SuperStar. This is an additional module of the Cambridge structural Database System that can be used to create a pharmacophore from an protein binding site. SuperStar uses knowledge on intermolecular interactions derived from the Cambridge Structural Database to create a hotspot map of the binding site for various probe atoms. These hotspots can also be converted to pharmacophores that can then in principle be used by a pharmacophore matching program to find candidate hits. For more information please see: http://www.ccdc.cam.ac.uk/products/life_sciences/superstar/ and http://www.ccdc.cam.ac.uk/products/product_flyers/superstar.pdf John Liebeschuetz - Applications Manager CCDC LEGAL NOTICE Unless expressly stated otherwise, information contained in this message is confidential. If this message is not intended for you, please inform postmaster*_*ccdc.cam.ac.uk and delete the message. The Cambridge Crystallographic Data Centre is a company Limited by Guarantee and a Registered Charity. Registered in England No. 2155347 Registered Charity No. 800579 Registered office 12 Union Road, Cambridge CB2 1EZ. From owner-chemistry@ccl.net Tue Feb 9 13:04:01 2010 From: "rocky walden rocky.walden19..gmail.com" To: CCL Subject: CCL: I have a question for you all Message-Id: <-41225-100209115910-28469-2NbaQmdzjXHCm+8GjNpz2w[]server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=0016e64980fe85457e047f2dd534 Date: Tue, 9 Feb 2010 22:28:59 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19 .. gmail.com] --0016e64980fe85457e047f2dd534 Content-Type: text/plain; charset=ISO-8859-1 Hiii People, I usually have lot of questions in my mind. The question that worries me is this thing How can we predict the Conformational energies of Cis Trans isomers in Cyclohexane using computational tools? By the energy values only we are able to tell whether Cis or trans isomer is stable. Let me know if there is any special techniques or theory appliccable. Is there any computational tool that does this work (free tool only Windows Version is preferable). Cheers rocky ROCKY !!! ROCKS --0016e64980fe85457e047f2dd534 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hiii People,
=A0 I usually have lot of questions in my mind. The questio= n that worries me is this thing
=A0How can we predict the Conformational= energies of Cis Trans isomers in Cyclohexane using computational tools? =A0By the energy values only we are able to tell whether Cis or trans isome= r is stable.
=A0Let me know if there is any special techniques or theory= appliccable.
=A0Is there any computational tool that does this work (fr= ee tool only Windows Version is preferable).

Cheers
rocky
ROCKY !!! ROCKS
--0016e64980fe85457e047f2dd534-- From owner-chemistry@ccl.net Tue Feb 9 15:47:01 2010 From: "Gonzalo Jim nez-Os s gjimenez/a\unizar.es" To: CCL Subject: CCL:G: I have a question for you all Message-Id: <-41226-100209154333-17039-zjW5eGd/7SBBmEIsJtBDqQ!^!server.ccl.net> X-Original-From: "Gonzalo Jim nez-Os s" Date: Tue, 9 Feb 2010 15:43:29 -0500 Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez,unizar.es] Dear CCL'ers, Is it me or the level of the questions submitted to CCL has decreased astonishingly in the last few months? I consider myself a young researcher and I am still a newbie in some aspects, but the main obligation I impose myself before posting a question is to carefully read and search about it in books, manuals, the web, etc. Of course, this includes software user's manuals and lists (I'm tired of deleting messages about Gaussian keywords and errors). I'm also a newbie professor and I'm experiencing the good and bad effects of the "Quick & Easy" concept which is being implanted in our students (and in our global society, I'm afraid): "just ask without thinking...anyone else will do the job for you. Copy-and-paste will do de rest". The conformational energies of cis/trans-cyclohexane? Seriously, what's that supossed to mean? Hopely, you mean "substituted cyclohexanes" or something...My advice on this: read a basic organic chemistry (at least a few pages) or ask your teacher/tutor before posting such questions. By the way, the answer is 'yes'. There are some "special techniques or theory appliccable", and even "free computational tools under Windows to do this work". Moreover, some of us use them (and also their non-free counterparts) to investigate on real chemical problems and (try to) publish our results. It has been said that some researchers even obtain public money to support their research. Can you believe it? Once the CCL was a reference in computational chemistry and one could read directly from the most relevant researchers in the field (unfortunately, they seem to be out the list these days). This is (intended to be) a serious scientific forum and not just the wall of facebook or twitter. Please, do not make me (and others, for sure) consider incoming CCL messages as spam. Peace out, Gonzalo PD. Is it really necessary to say "Rocky rocks!" at the end? Just think about it... > From: rocky walden rocky.walden19..gmail.com Sent: Tuesday, February 09, 2010 5:58 PM To: Oss,GonzaloJimnez Subject: CCL: I have a question for you all Hiii People, I usually have lot of questions in my mind. The question that worries me is this thing How can we predict the Conformational energies of Cis Trans isomers in Cyclohexane using computational tools? By the energy values only we are able to tell whether Cis or trans isomer is stable. Let me know if there is any special techniques or theory appliccable. Is there any computational tool that does this work (free tool only Windows Version is preferable). Cheers rocky ROCKY !!! ROCKS From owner-chemistry@ccl.net Tue Feb 9 18:57:00 2010 From: "zoran matovic zmatovic : kg.ac.rs" To: CCL Subject: CCL:G: I have a question for you all Message-Id: <-41227-100209185432-28526-mIkSbS9TapCqFKO7VatWDA[*]server.ccl.net> X-Original-From: "zoran matovic" Content-Transfer-Encoding: 7bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Wed, 10 Feb 2010 00:54:15 +0100 MIME-Version: 1.0 Sent to CCL by: "zoran matovic" [zmatovic*_*kg.ac.rs] Hello CCL's users, I have red Gonzalo's reply to "rocky" and (as before to similar debate) have a moderate attitude. May be Rocky has something else on his mind putting quest like this, may be he is young may be senior researcher may be unexperienced but has the right to ask for answer. His quest might be considered by computational chemists as silly one, wasting of e-mail space, a quest of one who did not read none of chemistry or comp chem literature or manuals or web pages, but he has the right to ask (this is free forum for everyone) and we may answer to or not to answer. Well, as far as we consider calcs of cis and trans conformational energies of substituted cyclohexanes there are plenty of literature and web pages (as Gonzalo said) and only what Rocky has to do is to: google or find wikipedia for the next words: conformational analysis computations then cis-trans or substituted cyclohexanes. Almost all elec. packages with HF/DFT or semiempirical or MM contain intro (manual) about conf analysis. Just give it try to find the part of interest. Have a very nice day (or night) all of you. zoran ----- Original Message ----- > From: "Gonzalo Jim nez-Os s gjimenez/aunizar.es" To: "Matovic, Zoran D " Sent: Tuesday, February 09, 2010 9:43 PM Subject: CCL:G: I have a question for you all > > Sent to CCL by: "Gonzalo Jim nez-Os s" [gjimenez,unizar.es] > Dear CCL'ers, > > Is it me or the level of the questions submitted to CCL has decreased > astonishingly in the last few months? I consider myself a young researcher > and I am still a newbie in some aspects, but the main obligation I impose > myself before posting a question is to carefully read and search about it > in > books, manuals, the web, etc. Of course, this includes software user's > manuals and lists (I'm tired of deleting messages about Gaussian keywords > and > errors). I'm also a newbie professor and I'm experiencing the good and bad > effects of the "Quick & Easy" concept which is being implanted in our > students (and in our global society, I'm afraid): "just ask without > thinking...anyone else will do the job for you. Copy-and-paste will do de > rest". > > The conformational energies of cis/trans-cyclohexane? Seriously, what's > that > supossed to mean? Hopely, you mean "substituted cyclohexanes" or > something...My advice on this: read a basic organic chemistry (at least a > few > pages) or ask your teacher/tutor before posting such questions. > > By the way, the answer is 'yes'. There are some "special techniques or > theory > appliccable", and even "free computational tools under Windows to do this > work". Moreover, some of us use them (and also their non-free > counterparts) > to investigate on real chemical problems and (try to) publish our results. > It > has been said that some researchers even obtain public money to support > their > research. Can you believe it? > > Once the CCL was a reference in computational chemistry and one could read > directly from the most relevant researchers in the field (unfortunately, > they > seem to be out the list these days). This is (intended to be) a serious > scientific forum and not just the wall of facebook or twitter. > > Please, do not make me (and others, for sure) consider incoming CCL > messages > as spam. > > Peace out, > > Gonzalo > > PD. Is it really necessary to say "Rocky rocks!" at the end? Just think > about > it... > > > >> From: rocky walden rocky.walden19..gmail.com > Sent: Tuesday, February 09, 2010 5:58 PM > To: Oss,GonzaloJimnez > Subject: CCL: I have a question for you all > > > Hiii People, > I usually have lot of questions in my mind. The question that worries me > is > this thing > How can we predict the Conformational energies of Cis Trans isomers in > Cyclohexane using computational tools? > By the energy values only we are able to tell whether Cis or trans isomer > is > stable. > Let me know if there is any special techniques or theory appliccable. > Is there any computational tool that does this work (free tool only > Windows > Version is preferable). > > Cheers > rocky > ROCKY !!! ROCKS> -------------------------------------------------------------------------------- No virus found in this incoming message. Checked by AVG - www.avg.com Version: 9.0.733 / Virus Database: 271.1.1/2677 - Release Date: 02/09/10 08:35:00