From owner-chemistry@ccl.net Fri May 7 07:26:00 2010 From: "matt j tassell mtassell**gmail.com" To: CCL Subject: CCL: Van Der Waals Complex Message-Id: <-41808-100507065848-21965-AneSJK6lo+Tu27W4mdsDmw##server.ccl.net> X-Original-From: "matt j tassell" Date: Fri, 7 May 2010 06:58:47 -0400 Sent to CCL by: "matt j tassell" [mtassell]_[gmail.com] Dear CCl I am currently looking at the addition reaction between a alderhyde radical and a molecule containing a double bond. I can find the transition state with no problem but i am having great difficulty locating the van der waals complex that comprises the two reactants. If i start at the transition state and lengthen the c-c bond that is being formed and re-optimize i find that i can only obtain the vdw complex with a small basis set (6-311G**)and b3lyp functional. I have read that i need to use diffuse functions to get an accurate description of the complex but as soon as i increase the size of the basis set either to 6-311++G** or aug-cc-pvtz (starting from either the original geometry or 6-311G** converged geometry) the forces converge but the displacements come nowhere near to converging. I have tried making the optimization convergence criteria very tight, change the step size and also using the gdiis algorithm, but none of these seem to make any difference. I suspect that the pes is very shallow and i am not describing it properly at the present. I was hoping that if somebody has encountered these problems before and managed to find a minima for the vdw complex they might be able to offer a suggestion as to how to best proceed from here? Many thanks in advance From owner-chemistry@ccl.net Fri May 7 08:48:00 2010 From: "Demetrios Xenides xenides|a|uop.gr" To: CCL Subject: CCL: Symposium on Clusters Message-Id: <-41809-100507084609-6708-RfXnB0r2drVyhZfpbeaQWA[#]server.ccl.net> X-Original-From: "Demetrios Xenides" Date: Fri, 7 May 2010 08:46:05 -0400 Sent to CCL by: "Demetrios Xenides" [xenides.]=[.uop.gr] We would like to bring in to your kind attention the following Symposium: "From Small Clusters to Functional Building Blocks of Novel Nanomaterials." ---Recent developments on the theoretical and experimental determination of the structures and properties of small, medium and large inorganic and metallic atomic and molecular clusters--- that is going to be organized during the ICCMSE 2010 (www.iccmse.org) in Hotel Kypriotis Village-Kypriotis Panorama-Kypriotis International Conference Center, Psalidi, Kos, Greece, 03-08 October 2010. We would, also, like to note that the Proceedings of ICCMSE 2010 will be published in the very famous AIP (American Institute of Physics) Conference Proceedings. Please find below a description of the symposium: Scope and Topics: Modern technologies not only require a vast diversity of new materials with well specified properties but also materials of small size which are able to combine more than one function in the same process. In order to fulfill this demand, complex systems with special properties owed to nanoscale morphological features or components have emerged as a very appealing solution. Their potential applications are outstandingly diverse and concern both genuinely new and existing technologies which range from microelectronics, and communication, to catalysis, optics and biomedicine. This diversity is one of the main reasons of the remarkable development of the field, widely known as nanoscience during the last two decades. The scientific and technological area of cluster chemistry and physics offers the prosper ground and the unique chance for both theoretical and experimental disciplines to combine their efforts. On one hand experimentalists need to explore new ways of producing in large scale crystals of high quality in the size of one billionth of a meter characterized by narrow size disparity and high emissive quantum efficiency. On the other hand, theoreticians have to try out old and new ideas aiming at a better understating of those nano-sized systems. The combination of these two disciplines is extremely vital nowadays due to the remarkable breakthroughs in the synthesis and the control of the size disparity the shape and the morphology of nanocrystalline which offer new perspectives in the research for novel materials for a wide range of technological applications. Proposed Topics --Structures and chemical or physical properties of small and medium clusters, nanoclusters, and nano-object. -- Synthesis and experimental characterization of clusters and nanomaterials. --Cluster based nanomaterials. --Clusters as functional building blocks of novel nanomaterials. --Magic clusters, Superatoms and Cluster assemblies. --New theoretical methods designed for the efficient study of large clusters and nanostructures. Best Regards, Demetrios Xenides From owner-chemistry@ccl.net Fri May 7 09:22:00 2010 From: "Anup Shah shahanup86*_*gmail.com" To: CCL Subject: CCL: Receptor Based Pharmacophore Model Message-Id: <-41810-100507063155-26659-w/8woSZc9t4otrb+srIBSQ-*-server.ccl.net> X-Original-From: "Anup Shah" Date: Fri, 7 May 2010 06:31:54 -0400 Sent to CCL by: "Anup Shah" [shahanup86:_:gmail.com] Dear all, Can anyone recommend me a tool for structure/receptor based pharmacophore model generation using various crystal structure of a receptor in different conformation? Thanking you in anticipation. ANUP SHAH M.S. (Pharm) Center for Pharmacoinformatics, National Institute of Pharmaceutical Education & Research, Sector 67, S.A.S. Nagar, Mohali Punjab-160062, INDIA From owner-chemistry@ccl.net Fri May 7 09:57:00 2010 From: "rocky walden rocky.walden19{}gmail.com" To: CCL Subject: CCL: Needed help in interpretation of the results. Message-Id: <-41811-100507063155-26636-aaExAbdRXqbgz6nLhhoCwQ,,server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=00504501572d8aeeeb0485fda632 Date: Fri, 7 May 2010 14:56:14 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19%gmail.com] --00504501572d8aeeeb0485fda632 Content-Type: text/plain; charset=ISO-8859-1 Hii CCL readers, I am using Turbomole, i have performed a calculation on carboxylic acid, I used Restricted Hartree-fock method and convergence factor used is 10-7, asked the application to calculate the NMR shielding. The job was successful it gave me an output file, its a human readable file but i am unable to interpret its results. i am here with pasting the results, if any one can help me in interpreting the results, can explain me briefly what are those values, i will be much thankful. $nmr rhf shielding constants # NO. TYPE MULT. ISOTROPIC ANISOTROPIC dD/dB-CONTRIBUTION 1 o 1 161.66655533 249.88593341 -233.44145446 2 c 1 36.06703273 169.33675006 -212.86538167 3 o 1 -85.83832058 624.85981932 -480.92857026 4 h 1 27.03601664 10.65610582 -2.21326829 5 h 1 24.99107514 4.78581852 -2.99780226 $end your help will be much appreciated. Thanks Rocky --00504501572d8aeeeb0485fda632 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hii CCL readers,

=A0 I am using Turbomole, i have performed a calcul= ation on carboxylic acid, I used Restricted Hartree-fock method and converg= ence factor used is 10-7, asked the application to calculate the NMR shield= ing.

=A0 The job was successful it gave me an output file, its a human reada= ble file but i am unable to interpret its results.
i am here with pastin= g the results, if any one can help me in interpreting the results, can expl= ain me briefly what are those values, i will be much thankful.


$nmr rhf shielding constants
#=A0=A0 NO. TYPE=A0=A0 MULT.=A0=A0= =A0=A0 ISOTROPIC=A0=A0=A0=A0=A0=A0=A0 ANISOTROPIC=A0 dD/dB-CONTRIBUTION
= =A0=A0=A0=A0 1=A0=A0 o=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0 161.66655533=A0=A0= =A0=A0=A0 249.88593341=A0=A0=A0=A0 -233.44145446
=A0=A0=A0=A0 2=A0=A0 c= =A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 36.06703273=A0=A0=A0=A0=A0 169.33675006= =A0=A0=A0=A0 -212.86538167
=A0=A0=A0=A0 3=A0=A0 o=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0 -85.83832058=A0=A0= =A0=A0=A0 624.85981932=A0=A0=A0=A0 -480.92857026
=A0=A0=A0=A0 4=A0=A0 h= =A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 27.03601664=A0=A0=A0=A0=A0=A0 10.656105= 82=A0=A0=A0=A0=A0=A0 -2.21326829
=A0=A0=A0=A0 5=A0=A0 h=A0=A0=A0=A0=A0 1= =A0=A0=A0=A0=A0=A0 24.99107514=A0=A0=A0=A0=A0=A0=A0 4.78581852=A0=A0=A0=A0= =A0=A0 -2.99780226
$end

your help will be much appreciated.


Thanks
Rocky=

--00504501572d8aeeeb0485fda632-- From owner-chemistry@ccl.net Fri May 7 10:32:01 2010 From: "rocky walden rocky.walden19]_[gmail.com" To: CCL Subject: CCL: Guidance in interpretation of the below results needed.... Message-Id: <-41812-100507075844-25765-Z+govhv+cFrGMa6Et5GKfg=-=server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=001485eba2e88e1bb00485ffc732 Date: Fri, 7 May 2010 17:28:37 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19|,|gmail.com] --001485eba2e88e1bb00485ffc732 Content-Type: text/plain; charset=ISO-8859-1 Hii CCL readers, I am using Turbomole, i have performed a calculation on carboxylic acid, I used Restricted Hartree-fock method and convergence factor used is 10-7, asked the application to calculate the NMR shielding. The job was successful it gave me an output file, its a human readable file but i am unable to interpret its results. i am here with pasting the results, if any one can help me in interpreting the results, can explain me briefly what are those values, i will be much thankful. $nmr rhf shielding constants # NO. TYPE MULT. ISOTROPIC ANISOTROPIC dD/dB-CONTRIBUTION 1 o 1 161.66655533 249.88593341 -233.44145446 2 c 1 36.06703273 169.33675006 -212.86538167 3 o 1 -85.83832058 624.85981932 -480.92857026 4 h 1 27.03601664 10.65610582 -2.21326829 5 h 1 24.99107514 4.78581852 -2.99780226 $end your help will be much appreciated. Thanks Rocky --001485eba2e88e1bb00485ffc732 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hii CCL readers,

=A0 I am using Turbomole, i have performed a calculation on carboxylic acid, I used Restricted Hartree-fock method and convergence factor used is 10-7, asked the application to calculate the NMR shielding.

=A0 The job was successful it gave me an output file, its a human reada= ble file but i am unable to interpret its results.
i am here with pasting the results, if any one can help me in interpreting the results, can explain me briefly what are those values, i will be much thankful.


$nmr rhf shielding constants
#=A0=A0 NO. TYPE=A0=A0 MULT.=A0=A0= =A0=A0 ISOTROPIC=A0=A0=A0=A0=A0=A0=A0 ANISOTROPIC=A0 dD/dB-CONTRIBUTION
= =A0=A0=A0=A0 1=A0=A0 o=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0 161.66655533=A0=A0= =A0=A0=A0 249.88593341=A0=A0=A0=A0 -233.44145446
=A0=A0=A0=A0 2=A0=A0 c= =A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 36.06703273=A0=A0=A0=A0=A0 169.33675006= =A0=A0=A0=A0 -212.86538167
=A0=A0=A0=A0 3=A0=A0 o=A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0 -85.83832058=A0=A0= =A0=A0=A0 624.85981932=A0=A0=A0=A0 -480.92857026
=A0=A0=A0=A0 4=A0=A0 h= =A0=A0=A0=A0=A0 1=A0=A0=A0=A0=A0=A0 27.03601664=A0=A0=A0=A0=A0=A0 10.656105= 82=A0=A0=A0=A0=A0=A0 -2.21326829
=A0=A0=A0=A0 5=A0=A0 h=A0=A0=A0=A0=A0 1= =A0=A0=A0=A0=A0=A0 24.99107514=A0=A0=A0=A0=A0=A0=A0 4.78581852=A0=A0=A0=A0= =A0=A0 -2.99780226
$end

your help will be much appreciated.


Thanks
Rocky --001485eba2e88e1bb00485ffc732-- From owner-chemistry@ccl.net Fri May 7 11:07:01 2010 From: "Lars Goerigk lars.goerigk|a|uni-muenster.de" To: CCL Subject: CCL: Van Der Waals Complex Message-Id: <-41813-100507091548-28893-uJ3bEazzPt7Q5faL5m7DeA:-:server.ccl.net> X-Original-From: Lars Goerigk Content-Transfer-Encoding: 7bit Content-Type: Text/Plain; charset="utf-8" Date: Fri, 7 May 2010 15:15:36 +0200 MIME-Version: 1.0 Sent to CCL by: Lars Goerigk [lars.goerigk:_:uni-muenster.de] Hello Matt, you definitely need some kind of dispersion correction for treating a vdW complex. Either you do this with a program that has e.g. the DFT-D correction > from J. Comput. Chem. 27, (2006), 1787-1799. Or you better have a look the new DFT-D3 dispersion correction from J. Chem. Phys. (2010), 132, 154104. (with a program that can be dowloaded from http://toc.uni-muenster.de/DFTD3/ B3LYP itself and other common density functionals are not able to correctly account for London dispersion effects. Cheers, Lars From owner-chemistry@ccl.net Fri May 7 11:50:01 2010 From: "Stephen Bowlus chezbowlus(a)comcast.net" To: CCL Subject: CCL: Van Der Waals Complex Message-Id: <-41814-100507103239-13372-pKOSwMJQ8w/jzq/xZm2oZA,+,server.ccl.net> X-Original-From: Stephen Bowlus Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes Date: Fri, 7 May 2010 06:58:54 -0700 Mime-Version: 1.0 (Apple Message framework v936) Sent to CCL by: Stephen Bowlus [chezbowlus-,-comcast.net] In other systems (and another program), I have used an IRC calculation to find the first minimum in the PES that (in my case at least) corresponded to the reactants' approach to one another. In my hands, IRCs are time-consuming, so you may want to may want to work with a small basis, or even use a semi-empirical method for a first try. -sb On May 7, 2010, at 3:58 AM, matt j tassell mtassell**gmail.com wrote: > > Sent to CCL by: "matt j tassell" [mtassell]_[gmail.com] > Dear CCl > > I am currently looking at the addition reaction between a alderhyde > radical and a molecule containing a double bond. I can find the > transition state with no problem but i am having great difficulty > locating the van der waals complex that comprises the two reactants. > > If i start at the transition state and lengthen the c-c bond that is > being formed and re-optimize i find that i can only obtain the vdw > complex with a small basis set (6-311G**)and b3lyp functional. I > have read that i need to use diffuse functions to get an accurate > description of the complex but as soon as i increase the size of the > basis set either to 6-311++G** or aug-cc-pvtz (starting from either > the original geometry or 6-311G** converged geometry) the forces > converge but the displacements come nowhere near to converging. > > I have tried making the optimization convergence criteria very > tight, change the step size and also using the gdiis algorithm, but > none of these seem to make any difference. I suspect that the pes is > very shallow and i am not describing it properly at the present. > > I was hoping that if somebody has encountered these problems before > and managed to find a minima for the vdw complex they might be able > to offer a suggestion as to how to best proceed from here? > > Many thanks in advance > > > > -= This is automatically added to each message by the mailing script > =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/> > From owner-chemistry@ccl.net Fri May 7 12:25:00 2010 From: "Sanjay Bharathwaj computationalchemist.:.gmail.com" To: CCL Subject: CCL: Method for Hydrogen Bonding Message-Id: <-41815-100506124958-20909-r/QrF3YEqxwUle6vJ3GFsg a server.ccl.net> X-Original-From: Sanjay Bharathwaj Content-Type: multipart/alternative; boundary=0016363b7dd02c290d0485eeda6b Date: Thu, 6 May 2010 11:46:55 -0400 MIME-Version: 1.0 Sent to CCL by: Sanjay Bharathwaj [computationalchemist%x%gmail.com] --0016363b7dd02c290d0485eeda6b Content-Type: text/plain; charset=ISO-8859-1 Dear Friends, Could you please let me know the methods either HF, DFT (if so which functional) that helps me to study the hydrogen bonded interaction. I find from literatures, that MP2/Lanl2dz provides the best.But i think it takes me long time for my system. In this regard, could you please let me know any other methods (computationally cheap) that help me to solve the problem. best regards, Sanjay -- Regards, Dr. Sanjay Bharathwaj Kumar, Dharmendra Institute of Technology, Andhra pradhesh, India. --0016363b7dd02c290d0485eeda6b Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Friends,

Could you please let me know the methods
either HF, DFT (if so which functional) that helps
me to= study the hydrogen bonded interaction.

I find fro= m literatures, that MP2/Lanl2dz provides
the best.But i think it takes me long time for my system.
In= this regard, could you please let me know any other
methods (com= putationally cheap) that help me to
solve the problem.

best regards,
Sanjay

-- <= br>Regards,
Dr. Sanjay Bharathwaj Kumar,
Dharmendra Institute of Tech= nology,
Andhra pradhesh,
India.
--0016363b7dd02c290d0485eeda6b-- From owner-chemistry@ccl.net Fri May 7 13:00:00 2010 From: "rocky walden rocky.walden19]^[gmail.com" To: CCL Subject: CCL: Receptor Based Pharmacophore Model Message-Id: <-41816-100507123219-23404-o80D67vVBtiLxWnyey+vTg__server.ccl.net> X-Original-From: rocky walden Content-Type: multipart/alternative; boundary=001485ebaa2a942f7e04860399c8 Date: Fri, 7 May 2010 22:02:06 +0530 MIME-Version: 1.0 Sent to CCL by: rocky walden [rocky.walden19*gmail.com] --001485ebaa2a942f7e04860399c8 Content-Type: text/plain; charset=ISO-8859-1 Dear Anup, U can try with PHASE ( SCHRODINGER tool) ( http://www.schrodinger.com/products/14/13/) U can also try with tool from Intel Ligand ( Ligand Scout) ( http://www.inteligand.com/) this is free tool for academics. thanks Rocky On Fri, May 7, 2010 at 4:01 PM, Anup Shah shahanup86*_*gmail.com < owner-chemistry,,ccl.net> wrote: > > Sent to CCL by: "Anup Shah" [shahanup86:_:gmail.com] > Dear all, > > Can anyone recommend me a tool for structure/receptor based pharmacophore > model > generation using various crystal structure of a receptor in different > conformation? > > Thanking you in anticipation. > > ANUP SHAH > M.S. (Pharm) > Center for Pharmacoinformatics, > National Institute of Pharmaceutical Education & Research, > Sector 67, S.A.S. Nagar, Mohali > Punjab-160062, INDIA> > > --001485ebaa2a942f7e04860399c8 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Anup,
=A0=A0 U can try with PHASE ( SCHRODINGER tool)=A0 (http://www.schrodinger.com/= products/14/13/)
=A0=A0 U can also try with tool from Intel Ligand (= Ligand Scout)=A0 (http://www.inteli= gand.com/)=A0 this is free tool for academics.


thanks
Rocky
On Fri, May 7, 2010 a= t 4:01 PM, Anup Shah shahanup86*_*gmail.com <owner-ch= emistry,,ccl.net> wrote:

Sent to CCL by: "Anup =A0Shah" [shahanup86:_:gmail.com]
Dear all,

Can anyone recommend me a tool for structure/receptor based pharmacophore m= odel
generation using various crystal structure of a receptor in different
conformation?

Thanking you in anticipation.

ANUP SHAH
M.S. (Pharm)
Center for Pharmacoinformatics,
National Institute of Pharmaceutical Education & Research,
Sector 67, S.A.S. Nagar, Mohali
Punjab-160062, INDIA



-=3D This is automatically added to each message by the mailing script =3D-=
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--001485ebaa2a942f7e04860399c8-- From owner-chemistry@ccl.net Fri May 7 15:17:00 2010 From: "Carlos F. Lagos carlos(-)cbuc.cl" To: CCL Subject: CCL: Receptor Based Pharmacophore Model Message-Id: <-41817-100507111134-17559-4PzlZAuaHsQwQECSAKDaxA__server.ccl.net> X-Original-From: "Carlos F. Lagos" Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 7 May 2010 10:37:19 -0400 MIME-Version: 1.0 Sent to CCL by: "Carlos F. Lagos" [carlos^-^cbuc.cl] Hello Anup, this is only one way you can do this. First superimpose all structures containing the ligand(s) to have them in the same coordinate space using any classical molecular modeling software, then use = LigandScout (www.inteligand.com, you can have one month free upon register to try = this approach) to generate a pharmacophore model for each one and add ligand = and pharmacphore to alignment, the you can cerate a shred feature = pharmacophore model for your study. Hope this helps QF Carlos F. Lagos Medicinal Chemistry Laboratory MCLab, Faculty of Chemistry P. Universidad Catolica de Chile=20 Av Vicu=F1a Mackenna 4860 I 7820436 Santiago-Chile Phone: +56 2 3541911 I http://www.quimica.uc.cl =20 =20 -----Mensaje original----- De: owner-chemistry+carlos=3D=3Dcbuc.cl/./ccl.net [mailto:owner-chemistry+carlos=3D=3Dcbuc.cl/./ccl.net] En nombre de Anup = Shah shahanup86*_*gmail.com Enviado el: Viernes, 07 de Mayo de 2010 06:32 Para: Lagos, Carlos F Asunto: CCL: Receptor Based Pharmacophore Model Sent to CCL by: "Anup Shah" [shahanup86:_:gmail.com] Dear all, Can anyone recommend me a tool for structure/receptor based = pharmacophore model=20 generation using various crystal structure of a receptor in different=20 conformation? Thanking you in anticipation. ANUP SHAH M.S. (Pharm)=20 Center for Pharmacoinformatics, National Institute of Pharmaceutical Education & Research, Sector 67, S.A.S. Nagar, Mohali Punjab-160062, INDIA -=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__________ Informaci=F3n de ESET NOD32 Antivirus, versi=F3n de la base = de firmas de virus 5095 (20100507) __________ ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com =20 __________ Informaci=F3n de ESET NOD32 Antivirus, versi=F3n de la base = de firmas de virus 5095 (20100507) __________ ESET NOD32 Antivirus ha comprobado este mensaje. http://www.eset.com =20 From owner-chemistry@ccl.net Fri May 7 15:52:00 2010 From: "Jiabo Li jiaboli:_:yahoo.com" To: CCL Subject: CCL: Receptor Based Pharmacophore Model Message-Id: <-41818-100507145509-19846-c1PLnQheUq39p9dpi+QvIQ[*]server.ccl.net> X-Original-From: Jiabo Li Content-Type: multipart/alternative; boundary="0-2008954560-1273254899=:42474" Date: Fri, 7 May 2010 10:54:59 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Jiabo Li [jiaboli%x%yahoo.com] --0-2008954560-1273254899=:42474 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable You can also check =A0 http://accelrys.com/products/datasheets/ds-pharmacophore-0308.pdf =A0 =A0 Jiabo Li --- On Fri, 5/7/10, rocky walden rocky.walden19]^[gmail.com wrote: > From: rocky walden rocky.walden19]^[gmail.com Subject: CCL: Receptor Based Pharmacophore Model To: "Li, Jiabo " Date: Friday, May 7, 2010, 9:32 AM Dear Anup, =A0=A0 U can try with PHASE ( SCHRODINGER tool)=A0 (http://www.schrodinger.= com/products/14/13/) =A0=A0 U can also try with tool from Intel Ligand ( Ligand Scout)=A0 (http:= //www.inteligand.com/)=A0 this is free tool for academics. thanks Rocky On Fri, May 7, 2010 at 4:01 PM, Anup Shah shahanup86*_*gmail.com wrote: Sent to CCL by: "Anup =A0Shah" [shahanup86:_:gmail.com] Dear all, Can anyone recommend me a tool for structure/receptor based pharmacophore m= odel generation using various crystal structure of a receptor in different conformation? Thanking you in anticipation. ANUP SHAH M.S. (Pharm) Center for Pharmacoinformatics, National Institute of Pharmaceutical Education & Research, Sector 67, S.A.S. Nagar, Mohali Punjab-160062, INDIA -=3D This is automatically added to each message by the mailing script =3D- E-mail to subscribers: CHEMISTRY ~ ccl.net or use: =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST ~ ccl.net or use =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message=A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml=A0 =A0 =A0http://www.ccl.net/spammers.txt--0-2008954560-1273254899=:42474 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
You can also check
 
 
 
Jiabo Li

--- On Fri, 5/7/10, rocky walden rocky.walden19]^[g= mail.com <owner-chemistry:_:ccl.net> wrote:

From: rocky walden rocky.walden19]^[gmail.com <= ;owner-chemistry:_:ccl.net>
Subject: CCL: Receptor Based Pharmacophore = Model
To: "Li, Jiabo " <jiaboli:_:yahoo.com>
Date: Friday= , May 7, 2010, 9:32 AM

Dear Anup,
   U can try with PHASE ( S= CHRODINGER tool)  (http://www.schrodinger.com/products/14/1= 3/)
   U can also try with tool from Intel Ligand ( Ligand= Scout)  (http://www.inteligand.com/)  this is free tool for aca= demics.


thanks
Rocky
On Fri, May 7, 2010 at 4:01 PM, Anup Shah shahanup= 86*_*gmail.com= <owner-chemistry ~ ccl.net> wrote:

Sent to CCL by: "A= nup  Shah" [shahanup86:_:gmail.com]
Dear all,

Can anyone recommend me = a tool for structure/receptor based pharmacophore model
generation using= various crystal structure of a receptor in different
conformation?
<= BR>Thanking you in anticipation.

ANUP SHAH
M.S. (Pharm)
Center= for Pharmacoinformatics,
National Institute of Pharmaceutical Education= & Research,
Sector 67, S.A.S. Nagar, Mohali
Punjab-160062, INDIA=



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--0-2008954560-1273254899=:42474-- From owner-chemistry@ccl.net Fri May 7 16:27:00 2010 From: "Bennion, Brian Bennion1^-^llnl.gov" To: CCL Subject: CCL:G: problem with SCRF optimisation Message-Id: <-41819-100507142322-10634-s7+WoDWt1ZmoLwJORpTQSw]_[server.ccl.net> X-Original-From: "Bennion, Brian" Content-Language: en-US Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset="iso-8859-1" Date: Fri, 7 May 2010 10:48:58 -0700 MIME-Version: 1.0 Sent to CCL by: "Bennion, Brian" [Bennion1%llnl.gov] Hello, Even slight modifications in the sphere radii governed by the "alpha" keywo= rd can help get past these sticky points in G03. In some publications this parameter is altered for charged species to obtai= n better results. Brian =20 -----Original Message----- > From: owner-chemistry+bennion1=3D=3Dllnl.gov.]_[.ccl.net [mailto:owner-chemistr= y+bennion1=3D=3Dllnl.gov.]_[.ccl.net] On Behalf Of Joaquin Barroso Flores joaco= _barroso/./yahoo.com Sent: Wednesday, May 05, 2010 1:20 PM To: Bennion, Brian Subject: CCL:G: problem with SCRF optimisation Hello, Aside the reccomendations by Pierre I would also advice to change the spher= e radii from UA0 to UAKS or even Bondy or Pauling. This can be performed by= adding the line: =20 radii=3Dbondi =20 after those numbers (OFac and RMin) suggested by Pierre; but in order to us= e all these parameters you have to use SCRF=3D(Read,...) in your route sect= ion. I have a post on some common problems in PCM calculations in my blog (= the address is below). Just in case you run into other issues since I know = the information online is somewhat scarce. =20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D Joaquin Barroso-Flores, Ph. D. Centro Conjunto de Investigacion en Quimica Sustentable Instituto de Quimica UNAM=20 Toluca, Mexico -> http://*joaquinbarroso.wordpress.com joaquin.barroso''a''gmail.com=20 "Blogastronom=EDa": http://*joaquinbarroso.blogspot.com=20 =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=20 ________________________________ De: Pierre Archirel pierre.archirel*|*lcp.u-psud.fr Para: "Flores, Joaquin Barroso " Enviado: mi=E9rcoles, 5 de mayo, 2010 13:15:50 Asunto: CCL:G: problem with SCRF optimisation Sent to CCL by: Pierre Archirel [pierre.archirel_-_lcp.u-psud.fr] This is an answer to A. Kuznetsov: I had the same issue many times with Gaussian 03, I solved it through performing a first optimisation with one of the three possibilities: 1- add the nosymmcav keyword (if you a have symmetry) 2- add the following additional keywords: ofac=3D0.8 rmin=3D0.5 which makes the cavity much simpler 3- add the noaddsph keyword (very drastic) In every case, take the optimised geometry and optimise again with your first options. Pierre Archirel PS gaussian 09 is much more robust in this respect ____________________________________________________________ ATTENTION MON ADRESSE ELECTRONIQUE A CHANGE: VOIR PLUS BAS Pierre Archirel Groupe Th=E9osim: Th=E9orie et Simulation Laboratoire de Chimie Physique Tel: 01 69 15 63 86 Bat 349 Fax: 01 69 15 61 88 91405 Orsay C=E9dex France pierre.archirel,+,u-psud.fr ____________________________________________________________ -=3D This is automatically added to each message by the mailing script =3D-the strange characters on the top line to the ^^ sign. You can also E-mail to subscribers: CHEMISTRY^^ccl.net or use: http://*www.*ccl.net/cgi-bin/ccl/send_ccl_message E-mail to administrators: CHEMISTRY-REQUEST^^ccl.net or use http://*www.*ccl.net/cgi-bin/ccl/send_ccl_message=3D =20 Before posting, check wait time at: http://*www.*ccl.net =20 Job: http://*www.*ccl.net/jobs Conferences: http://*server.ccl.net/chemistr= y/announcements/conferences/ Search Messages: http://*www.*ccl.net/chemistry/searchccl/index.shtmlhttp://*www.*ccl.net/spammers.txt RTFI: http://*www.*ccl.net/chemistry/aboutccl/instructions/ =20 From owner-chemistry@ccl.net Fri May 7 17:02:00 2010 From: "Nuno A. G. Bandeira nuno.bandeira . ist.utl.pt" To: CCL Subject: CCL: Method for Hydrogen Bonding Message-Id: <-41820-100507140604-5171-9rDjRORZGea7S+n2+5oVKg__server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 07 May 2010 19:27:00 +0200 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira[-]ist.utl.pt] On 06-05-2010 17:46, Sanjay Bharathwaj computationalchemist.:.gmail.com wrote: > Could you please let me know the methods > either HF, DFT (if so which functional) that helps > me to study the hydrogen bonded interaction. > > I find from literatures, that MP2/Lanl2dz provides > the best.But i think it takes me long time for my system. > It's not a guaranteed bet that you'll get a proper description of the H bond using DFT but you could try Barone's modification of PW91 aka mPW91, or PBE or any functional using Grimme's empirically dispersion corrected DFT-D methodology. Also make sure you add enough polarisation functions to your atoms (simple LANL2DZ might not be enough). Best wishes Nuno -- Nuno A. G. Bandeira, AMRSC Laboratoire de Chimie LR6 Ecole Normale Superieure de Lyon 46, Allee d'Italie 69364 Lyon Cedex 07 - France http://cqb.fc.ul.pt/intheochem/nuno/ --